There's legitimate reasons to not run R&D mode. Honestly the only reason I've found in the long term to run it is when hardware bugs (the little internal capacity/batter doesn't charge, so if you let the battery discharge it starts to boot loop instead of actually charging when it gets bad enough - turning on R&D mode avoids that), or software bugs (on my first N900 it seemed that the watchdogs or the lifeguard reset killed stuff). But besides that I happily ran without R&D mode on my N900s for a long while - I used to say everyone should be running it too, but honestly I don't really have strong reasons to advocate either way... but I kinda mellowed out with regard to that position over time.
Did you forget my rdmod utility? That'll turn your R&D mode on for you right on-device.
Funny enough lots of people do, actually. You know, they're not exactly app stores, but they use the distro-provided GUI wrapper around the actual package managing stack.
Like 'fkdep', perhaps?
How did this end up going?