Is it possible to reprogram this while it is inside the Macintosh? Do your MACSIMMs come pre-programmed with the 0.9.6 version which supports the ROMDriver Control Panel?

Unfortunately it is not possible to reprogram the SIMM in system.
The SIMM can be programmed using Doug Brown SIMM programmer or by removing the chips and using a standard EPROM programmer.
I usually ship the SIMM with the 0.9 driver (this supports ROM disk). If you prefer a more recent one, I can flash any image you like. Please make sure you test it with an emulator first.

Ideally I'd like to get a flash programmer so I can experiment with more than just the ROM disk, but maybe also making modifications to the ROM eventually. Would you provide a recommended tool that I can purchase relatively cheaply and tutorial at least to start out with testing custom ROM disk images?