I agree with you on all points here. But chicken or egg.. or none till you take a day and do it all..
I've read 8 HP on the TB upgrade.. I'd guess it a 5-8 increase..
And granted the stock system falls short of being able to supply all the air the engine can ingest .. at full throttle.. but that doesn't mean a larger TB wont gulp in that available air a little faster.

And as far as a tune.. it's been noted several times that the computer has enough variance to compensate these mods. A tune is not even necessary.

Mine was done in stages.. K&N stock box
Throttle body
Replaced K&N stock box with 3" tubes to cone filters
And finally tossed in the tune.
With 2-3-4 months between each phase.

No adverse performance or issues anywhere along the path taken here. And each one was just a baby step to performance to the whole package per say.