The Fate Freeport Companion is a modern mechanical update for a setting from 2003; the Fate SRD is the newest version of the Fate engine, released in 2013. You will find discrepancies in the implementation of each system's ethos. Additionally: until last year's release of the Fate Core System book (the Fate SRD is this book in SRD form), there was no universal Fate engine. Every version of Fate was a setting-specific version of the Fate concept, with unique variants adapted for that setting. The Companion, while using Fate Core mechanics, feels free to make setting-specific choices about how to implement those mechanics for a Freeport experience
In this case, the Fate SRD breaks from most earlier iterations of the Fate engine in its default handling of NPC Fate points: even relatively recent systems like the Dresden Files RPG (which was considered the most up-to-date example of the Fate engine until the Fate Core System book) used the character creation rules to give Fate points to individual NPCs, just like Freeport does. As you've seen, the Fate Core System book on which the Fate SRD is based now defaults to a single Fate point pool shared among all NPCs. The Freeport Companion keeps the older tradition.
[...] while Companion is intended to give you all the nuts and bolts you need to explore the mean streets of Freeport, you shouldn’t feel obligated to use all the information provided in this sourcebook. [...] The rules included here are designed to be modular, meaning you can take what you like and leave the rest. (FFC6)
Because Fate is composed of dials you can adjust to meet the needs of your group, feel free to give named NPCs their own Fate point pools if you think that's a better fit for your own game experience. DFRPG included the "shared NPC pool" option as a variant, and likewise you should feel that the "separate NPC pools" is an available variant for your game. (And since it is a dial, there is an intermediate option: Single pools for each major threat in the story! One pool for every threat related to the Autocratic Empire Spanning Galaxies, one for every threat related to the Rapidly Growing Vampire Population, and one pool for threats related to Cthulhu is Coming --if those are the Threats in your game.)
The major difference lies in whether the story treats all opposition to the players as a single continuous multifaceted entity (Fate points granted to one NPC can be spent by another) or if the story considers each challenge the NPCs face to be its own unique entity (NPCs can only use Fate points they earned themselves). I prefer the communal NPC pool because it's simpler for me to keep track of and because Fate points spent on characters who turn out to be non-recurring don't just vanish from the Fate economy.