Less book-keeping and easier to explain
You are correct in a few things. Capital checks are made per building and not per room, but nothing stops you from owning multiple rooms that are each their own building, and consequentially, their own business.
However, keep in mind that managing each business also becomes a problem. That is because you (the character) can only make a single check to earn Capital (as opposed to income), so if you are going to create Goods, you will make a single check per day using a single room, since you cannot occupy more than one building at once. So, while it's a good idea to own multiple buildings to earn income, it's not always a good idea to own multiple buildings when trying to earn Capital, as one building with multiple rooms can have a bigger bonus to your check.
Otherwise, you will have to explain to the GM how those "empty rooms" are generating their Goods, Influence or Magic:
If you intend for your building or organization to generate capital, you must explain to the GM how it does so.
To clarify, I say they are "empty", but they are technically being operated by unskilled laborers, and there is just so much that those people can do. The GM might say that they have a bad working condition (being confined to a single room all day, for instance) and prohibit such operation from going on without consequences. Which is why those unskilled laborers are usually limited to generate income instead of anything more complicated than that.
If you say that you are renting those rooms, and later must make a capital check to earn Goods, it wouldn't make a lot of sense that those people would suddenly work for you for free.
So, there is a bit of GM fiat on what can be done there. It's easier to explain a well-constructed business than multiple separate rooms doing separate stuff on their own.
If you are going to run organizations like a team of smugglers or a group of acolytes, you must provide them with the necessary buildings so they can operate. Otherwise, their income is halved:
If you don't provide a building for the team to work in or from, halve the Earnings for that team.
Combining all those rooms into a single business will allow you to have an easier time registering your downtime activities. Otherwise, you will have to bring a spreadsheet to the game table so you guys can control all of that. Especially if each room is doing separate capital checks.
Higher stacked bonus for capital checks
When combining rooms you also benefit from a higher stacked bonus to your capital checks.
For instance, owning multiple Alchemy Labs will allow you to make multiple checks with +10. How exactly are you earning that is open to you and your GM to decide and the GM may veto your methods or not. If allowed, and you are trying to earn capital, each room can make their own check and will earn up to two capital per check (taking 10, for a total of 20) per room. Owning 10 labs will allow you to earn up to 20 Goods or Magic capital per day, while owning a single building with 10 labs will allow a single check with +100 that can earn up to 11 Goods or Magic per day.
A Scriptorium, on the other hand, doesn't have such a high bonus (+5), and each check can only create up to one capital per day. Adding a Storefront (+5 to any capital) to the same building will result in the same benefit as being separate buildings (one capital per day), for a total of two capital per day, so the only reason for them to be separate buildings is when you are using them to earn income (gp), as they will grant the same benefit in capital to you.
And also because you need one Manager for each business if you are going to stay away for longer than a week from your buildings and organizations.
For every 7 days you were away from the settlement (whether downtime days or normal days), reduce your Goods, Influence, Labor, and Magic by 1 each (minimum 0). This decrease represents spoilage, theft, allies moving on or having higher priorities, workers finding other employment, and so on.
Otherwise, the attrition generated will be too big and you might lose control of a bunch of your stuff. After a while (30 days), you might even lose your buildings.
Because adventuring is dangerous work, if you're away from a settlement for 30 days or more, you risk losing control of your businesses there as employees begin to wonder whether you're dead. Upon your return, you must attempt a leadership check (1d20 + your Leadership score) against a DC equal to the number of days since you last had contact with that businesses — 10 (so if you've been gone for 30 days, the DC is 20).
In other words, if you are going to build 10 rooms as 10 separate buildings, you will also need 10 managers, which will offset any benefit of those rooms and you probably won't earn any money from it at all.
Again, earning capital on multiple business becomes a problem on small settlements due to the Spending Limit of those settlements:
The population of a settlement limits how much help you can get on a given day. The following numbers represent the limit of how much Goods, Influence, and Labor you can utilize in settlement each day. Even if you have a lot of Goods and Labor at your disposal from favors and such, a tiny settlement might have only a few hands to spare to turn that capital into finished projects.
So, in a Village, the most capital you can earn in a single day is 10, no matter how many rooms and buildings you got trying to earn that same capital. Meaning that in a Metropolis, you cannot have more than 65 total business going on for the same type of capital, you will have to either split your capital checks to keep benefitting from all your buildings.
Less downtime events
Yes, having multiple Downtime Events occurying all at once can ruin your day if you are specially unlucky and/or your settlement has a high Danger attribute.
If you're using the settlement danger value, add the danger value to the percentile roll.
And those unskilled laborers can't do much when a check is asked for:
Many events allow a skill check to affect the outcome of the event. If you're present, either attempt this skill check yourself or ask another member of the party or a manager to attempt the check for you. If you're absent, either your representative (such as a cohort or manager) attempts the check or roll 1d20 with no bonuses to determine the result.
So, while a village has a lower chance of dangerous events, a metropolis has a higher chance of something bad happening to every one of your buildings.
Also, remember what I said about book-keeping? The GM will quickly get tired of rolling so many events for every single building of yours and either he will start to decide that you gotta make a single check and will have to combine your business so you guys play pathfinder instead of Sim City RPG, or he will roll a single event for all your business, which could be catastrophic if something bad happens.