Would be easy to make optional at quit time, but the idea was to kind of make the feature automatic without user involvement in cases where say, Windows does a shut down at 3am to install a patch or similar.
You should not have to delete lastexit.sim to start multiple instances. Yes, each instance will start up with the same lastexit sim file but you should then be able to open whatever sim you want in either or both instances. Yes, when you close the two instances, the last one closed will overwrite the lastexit.sim, but lastexit.sim should not be used as a replacement for manual saving or autosaving of sims. It's just there as a safty net. People running complex, multi-instance sims should save them explicitly to their own sim files, manually or automatcially.
2.43m will fix the bug with colors and species selection. I will try to post that today (west coast US time).