Well maybe it was a one-time glitch. I repetead the experiment and it seems like "remove/will remove" and "install/will install" behave as expected.
Still, I hate having to wait to transfer recently updated apps from my iDevice to computer. I set my iTunes to automaticlly download everything. but it seems it doesn't do it before syncing.
Bottom line, the "sync apps" box in iTunes 10 was good and it is gone from iTunes 11.
seems I found the "check box" finally!!!
That's in iTunes > Preferences... > tab "Store" > section "Automatic Downloads" in the middle, there is a check box "Apps". Switch that off and then click "OK". However, please be careful that it seems need some time (after click "OK") to really store the updated preference. It would be better to first double check by selecting Preferences again.
Then plug in the iPhone/iPad, it'll first *CONTINUE* the step 7 if you ever cancel it in the last sync. Please wait patiently until it finished (which already ruinned your App list in iTunes, sorry for that). Then in the next sync when the iOS device plug in, step 7 would never appeared again.
Thanks for taking the time to reply.
It seems to be working fine now (all automatic were off when I did the first sync).
It may have been a one time glitch because of the unusual way I set up my iTunes on the new computer (manually copy the folder from the old computer) and/or simply the upgrade from iTunes10 to iTunes11 just does not go smooth. I am saying that because the new "app sync" paradigm in iTunes11 is different from iTunes10 (I like it better).