Best way to think about it is that in Empires the heavy infantry portion of the legion come as a package. So if you like the legion counter is around 4-5,000 heavy infantry (and what these are varies across the game). The Velites are a skirmisher unit so have a different role so are represented differently.
I agree that in the early Republican legion, they were incorporated so this is a pragmatic way to reflect the different roles on the battlefield.
FoG2 has a conversion system, that takes into account the basic Empires troop type, fatigue, leadership, hit points etc. So the 'legion' appears as a variable number of cohorts some hastati/princeps and some triari. Its variable because if you have a huge battle (say 600+ power on each side) then the number of individual FoG2 units are reduced (each has more manpower) just to make it manageable.
You can mod the conversion rules as you wish, but you don't directly choose from an army list. The result is great actually, you end up with a far greater range of troop types (incl some that are really rubbish), on terrain not of your choosing and have to get on with it.
This produces some very unique and tricky battles, I did an Armenia test and most battles in the first century or so were basically clashes between second rate (training and equipment) army until the better trained Seleucid or Antigonid armies showed up. Later on when I'd created the basis for a good Armenian army then I had an interesting mix of cataphracts, bows, imitation legions and lots of not very good medium/light troops. All this generated automatically.
it works really well, but any details will either be in a DD or have to wait for release