Mac App Store updating apps on _other_ drive :-(

A little background first - wanted to not just jump right in in upgrading to Mountain Lion (10.8.0), so I got (same brand) external USB HD, formatted it, installed Mountain Lion on that. (With some assistance from Apple Support...) I have moved most all my apps and documents over to the (external) ML drive (500GB). Also have many apps bought through MAS and installed on the ML-500 external drive. When I want to use ML, I boot up from it; other times, I will boot up with Snow Leopard (10.6.8) on the internal drive (320GB) to use a few apps where I haven't had all their docs transmogrified to 10.8-compatible apps. Most of the time now, things have been workable and fine.
In the past couple of days, I have discovered that apparently when I had logged into the MAS to update my ML-compatible apps, the MAS (unbeknown to me) updated the older (10.6.8-compatible) apps I had there, including iWork '08 (which had been updated as far as 10.6.8 updates would take them).
So now, it appears (since version numbers are the same for the Numbers, Pages and Keynote apps between the two OS drives) that I have (non-10.6.8-compatible) apps on the Snow Leopard (internal) drive, that won't run when I start up with 10.6.8. The icons on the 10.6.8 drive for Numbers, Pages, and Keynote (which were inside an iWork '08 folder, inside the Applications folder, on the internal/10.6.8 drive) have the 'not' circle and line across them when I view them running from the Mac OS X 10.6.8 (internal) drive. Haven't checked other MAS-downloaded 10.6-compatible purchased apps, so there may be more 'over-updated' apps...
I know that I have my original iWork '08 DVD (and likely, can go back through my Time Machine backups to try to find my latest versions under 10.6.8) and can re-install (and then install all the updates since then under 10.6.8) to get them back, but I would think  - since OS X install discs check a drive for the system version number before installing - that MAS would be setup to FIRST check what the OS X version for a drive with Pages/Numbers/Keynote/other Apple non-system apps, before installing a version over an app (that renders it useless for that version of OS X).
Even though I can possibly (with much time/updates/re-installs) get my earlier apps back on the internal drive, my concern is - how can I stop MAS from once again 'over-updating' those apps? If the MAS can check and tell me that an app I want to download requires 10.7 or 10.8, it would seem to make equal sense for it to check first whether I have (on different drives) 10.6.8 and 10.8 versions of the same app, and ONLY update the most recent one, NOT all of them.
Makes me wonder if Apple thinks that NO ONE out here is running separate partitions or drives with different operating systems for different app needs. I am very sure that there are specfic-market applications out there that companies, laboratories and others need to get tasks done (and for which there is not yet so far a Lion or Mountain Lion-compatible version), so those people/companies/etc. are likely running different OS partitions or startup drives. So WHY does the MAS not check first? Or more importantly, is there some way to stop/limit the updates so ONLY one drive gets updated?

Hello Dahveed, thank you for your answer but this is not good at all. These are not core applications. For instance i want all my games to be on external Hard drive (for instance X3 is about 8 Gb). For having my home folder on external HD this is not good at all too.
Why i should change my way to work and manage my files just for a logical problem ?
Furthermore, the Mac App Store app detects i have the application already installed even if it is on external HD, so there are only 2 solutions : there is a bug into the mac app store application for managing apps OR this is pretty bad for users to have the apps sequestrated into the home folder.
You can see even iTunes with the music rights management system is able to let you have musics managed by user.
Do you have another solution ?
Thank you

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