A good font manager should help.
I'm a big fan of Suitcase Fusion 4. I don't think there's anything really close to it on Windows. There's a free trial available at Extensis.com.
You don't mention what you font manager is.
I use MainType. You can uninstall the MS fonts on an individual bases (don't uninstall Segoe), or better include them in a library and turn the library off. MT will show home nay characters/glyphs are included in a particular font, sans any composite characters.
Download the trial and see if it fits your needs.
In terms of fonts that Windows 7 installs in its C:\Windows\Fonts directory, you delete, move, or manage those at your own risk. Some are required by Windows itself and others are assumed to be available by applications from Microsoft and others. Be careful.
You should also be aware that many system vendors install their own “added value software” on new systems in addition to Windows itself. (Some would designate some of this dubious “added value software” as shovelware.) Such software may also install fonts. Personally, I've seen some such software add upwards of 50 to 100 mediocre typefaces to the system. All such fonts are certainly deletable assuming you either delete the shovelware, don't use it, or at least don't use the funtionality that calls upon such fonts.
In terms of what you describe as autofill on fonts, Windows and various Windows applications do have a function by which any “missing glyphs” in a font are filled by comparable glyphs from some other system font per configuration in the Windows registry. You actually see this using the Character Map utility where it appears that all fonts have all glyphs (or at least all TrueType fonts have all glyphs).
The good news is that within Adobe applications, such autofill as you describe it does not occur. You get the pink box. To see what glyphs are actually defined in a font, you should look at the glyphs panel for the font in question. Only the glyphs actually defined in the chosen font will appear.
Congrats to Microsoft for making these available, but they're not optional; they're installed in the Windows\Fonts folder, and marked as system files, so if they're moved to another location (with the intention of handling them with a Font Manager and making them available on-call) the system just restores them in the folder at the next reboot. In the meantime, they clog the installed fonts list — most of them, uselessly, for any individual user. Is there any way of bringing these under control?
I actually use all of those fonts on a daily basis (working in a translation firm, of course!) but I do recall that Win7 lets you hide fonts you don't want to see, specifically because people who aren't doing lots of multilingual work are hampered by having to scroll past a million fonts intended mainly for complex-script support.
Looks like you should be able to get there from your Fonts menu:
Hm, never mind - looks like the phrase "These settings might not apply to all of your programs" means "These settings will only apply to the latest Microsoft applications, anything non-MS or older than 2010 will still see all the fonts even if you check this box."