I didn't try a direct-connect to the bike's 12V for the reasons you gave, fearing it would fry the cheap circuit board on the remote. Instead, I just retained the 9V battery inside the remote, then re-wired the button to another momentary switch on the dash. Now I just push the switch on the dash and the garage door opens. I use a Radio Shack #275-644. It's rated for 125VAC but it works fine for 12VDC, and so far water hasn't affected it.
I installed the remote first on my old RK under the right side cover, now inside the fairing on the SG. Since 1998 I've changed the 9V battery in the remote only once, and that time only after about five years as a precaution, so the battery going dead has never been an issue for me. I would change it every few years at an opportune time when you have easy access to the remote, but I've taken it for granted so long I will face a dead battery one of these days.
For those cases when a remote isn't available I rigged up a high-security switch (SPST on-off type) near the garage door. If necessary I can insert the barrel key, which I have on all my key chains, and open the door. It's a very simple wiring procedure, connecting to the existing push-button switch in your house in parallel.