Over the top of the shopping centre they have there, with the bufferstops level with the Eurostar ones. The FCC station could also be much improved, so it wouldn't look and feel like a neglected sub-basement.
It's ridiculous how far you have to walk from the tube to the EMT platforms, but I'm sure all the high-priced eateries and boutiques appreciate all the commuters that have to walk past them everyday.
There's not room, that's why the EMT and SET platforms extend further out past the sides of the original building. Also, if you put the buffers stops there, you have an extra two hundred yards of track that's not needed.
And even if you could do that, the bottom floor would be so dark as to be no use, so you then have to find somewhere for Eurostar check-in, security, arrivals etc. Unless you just use artificial light throughout which will cost a bomb, and no retail at all, which means a loss of revenue for the railways.
FCC is where it is, because that's where the line runs. Yes, it's downstairs but what else would you do? It's bigger than King's Cross Thameslink, with wider platforms, better access (escalators and lifts).