Hello,
The reason we added it was because without having then all removed first, there were absolutely countless support emails about frontpage not working.
Any weird setting in the .htaccess files will break frontpage totally, so they're all removed. I'm pretty sure we're not the only ones who do it that way.
If a user goes the frontpage route, then they're recommended to stick only with frontpage for file upload and not muck about with doing things manually on top of that for permission reasons, or changing files they shouldn't be. (the fact that they're using frontpage in the first place may indicate they're not as farmiliar with manual things, and have a higher tendancy to break things)
Yes, you can edit the htaccess files after you enable frontpage, but FP has several settings it needs to be exactly a certain way, so having other things setup ahead of time is far more likely to break.
John