I’ve experienced a similar “changed hardware, lost feature” with an older NLE on my Amiga. Updating from MovieShop4 to MovieShop5, also required updating hardware. With the old hardware, there was a real-time chromakey feature. But it was lost along the way with chipset changes & upgrades for the new hardware. The new system was definitely worth it and feature rich but many lamented the loss of the real-time chromakey that now had to be duplicated with software rendering.
The latest version of Media100 offers a lot of new features that make it worthwhile. There are Media100 re-rendering options that can achieve what you want to do with custom re-cropping but certainly not as ideal as the realtime hardware solution of yesteryear.
I use Sorenson Squeeze when I want to crop & reframe my raw footage before bringing it into Media100. I need to convert the MTS files anyway before using Media100. For a straight quick conversion, I use Clip-Wrap. For other needs, like crop/reframe/etc, I use Squeeze to make prores files.