I haven't been able to find a RAW answer on this, so I'll just tell you how I've handled this in the past.
- For multiclassing, I just ignored the penalty.
- For crafting, I gave the characters a certain amount of accrued xp per level (I think it was 25% of the xp it would have taken to reach that level the normal way) that they could expend for crafting without leveling down or delaying levels.
Here's why - to me, the purpose of milestone leveling is to:
- Simplify the process of tracking xp
- Allow leveling to feel like a reward for a meaningful accomplishment (rather than being 400xp short at the end of the dungeon and having to wait until the next minor fight).
- Allow control over how fast the party advances
- (for some parties) Ensure all players are at the same level
Trying to account for multiclassing or crafting penalties would conflict with those purposes. It goes back from being simple to being a nightmare (I'm honestly not even sure how you'd manage a multiclassing penalty in that system). It also removes the aspect of meaningful accomplishment: "You all level up after escaping the temple of doom! Except you - because you're multiclassing, you'll level up partway into the next adventure".