Neither the A4000D/CD32 version, nor the A1200 version will fir in an A4000T.
Kolla, the black borders are an artefact of your flatscreen. Indivision cannot do very much about it, other than trying to move away from the standards, which confuses most monitors (as you're writing, your monitor displays the "out of range" message).
If you're having difficulties displaying Super72, please install the latest update. Only the very first revision that was delivered in summer of 2008 had problems with Super72. All Indivision AGA models can be flashed with the latest updates, it's re-configurable hardware, so hardware updates are possible by installing a new flash version.
Switching between "always over 60Hz" and "legacy flickerfixer type 49.9Hz mode" is done with the scanrate: Rate 1.00 is the legacy mode and scanrate 1.25 is the new "always over 60Hz" mode. Of course, this only means "always over 60Hz" if you're displaying a standard Amiga mode. The HighGFX modes almost all require the 1.25 scanrate setting and not always output 60+Hz.
Chipram usage with Indivision is equal to chipram usage without. However, with flicker-free 24-bit display in all modes, it's tempting to choose a mode that eats more chipmem. It's like a ride in a sports car: You're tempted to use just a little more gas than you'd do in an economy car :-)
About odd screen aspects, did anyone notice Ratte's HD720 mode?
Jens