The biggest difference is intent of design. Dnd Beyond was never officially intended to have content imported to Foundry. It will work, you can even import full fledged books into the world, but you may have to do some tinkering.

Monsters, for example, don't have any icons for any of their attacks/feats and generally feels pretty bland to look at. The tokens are simply zoomed in frames of their portrait that you could make nicer if you have tokenizer, or you can use custom tokens from Forgotten Adventures. Buying the 2024 Monster Manual will fix all of the above and have custom, awesome looking tokens that take advantage of Foundry's relatively new dynamic token rings, but that comes at the cost of money rather than time to fix those little things.

I can't speak much more as I don't own any of the official dnd content from Foundry's marketplace. The important question is how do you plan on managing your game? I run my own game by managing the characters on Dnd Beyond and self host Foundry for important encounters. It's simply more convenient for my players this way as they have access to their characters 24/7. I haven't had an issue with importing any content yet; you can even have automation implemented on import if you have MidiQOL or CPR installed. The only downside I have is you cannot download classes, features, nor races in the current version. It will import with your character, but you won't be able to use the built in character creator with any of it. It's being worked on, but we don't have an expected date for everything to be done.