Really cheaper to buy upper/lower separately?

Buying the lower/upper separately is most definately cheaper, but not necessarily from a company that mostly deals with complete guns (RRA, Bushmaster, etc.)

Superior Arms or Stag Lower: $90+transfer.
LPK: $55
Stag M4 upper from Ranier Arms: $425
Buttstock $75-$90.

$660-$700, depending on options, and the gun will be as good as anything RRA makes. Stag's M4 uppers are top-notch.

Or, go with a Del-Ton complete kit on a SA lower and you can do the whole gun for under $600.00.

order a kit from Del-Ton:
http://www.del-ton.com/Rifle_Kit_p/rkt104.htm
About $620 set up the way you want and a stripped lower for about $100.
Put a half hour of work into it and you have the rifle you want for about $725.

Generally if you shop around you can get it done for a bit cheaper..

I'd like to get 1 lower and then buy a few different uppers, flat-top .223, maybe a flat-top .22LR etc...Then depending on whats cheap at the time I could shoot that calibre.

I'm looking for flexibility.

One reason its cheaper to buy upper and lower separate is because there is a Federal Excise Tax on firearms (of something like 10% ... I don't know the exact amount).

So if you buy a complete firearm, you pay the excise tax on the entire price. If you buy just a lower (which is the part of the gun that the law considers to be "the firearm") you only pay the tax on the price of the lower.

You can buy gun parts all day long and pay no excise tax, but as soon as there's a lower receiver (or upper receiver in the case of a FAL) you pay tax on the whole bill.

Also, you pay a little more for a complete firearm than for the parts because you're paying for its assembly (although I can't imagine there's much assembly with an AR)