I removed my water heater to put in a new one (although I haven't put in the new one for some years as I use the area for storage instead), but... yes... I noticed a few annoying features.
First of all, do you mean fiberglass when you say "plastic" pan? Mine has a nice, molded fiberglass pan. Anyway, I took care of a few issues I noticed:
1) Outer trim/door was put on with silicone. WHAT A BEAR to remove (also bent the door in doing so, but I had already ordered a new one). Won't be repeating that stupid mistake. Thank goodness Chinook only seemed to fall for the silicone trap on that one place (Suburban did specify it, but come on, don't take the bait!).
2) Fastening screws went into teensy-eensy little plywood strips that were barely hanging on (or not) with polyester mush. Larger pieces of epoxy coated wood epoxied on is an improvement.
3) Suburban specifically says NOT to use any screws through the bottom pan (for obvious reasons as water comes in there), but Chinook did use two screws through that area (screws are only supposed to be on sides not bottom). I filled the holes with thickened epoxy and will not repeat that.
4) It's been a few years, but I think there might have been a slight gap between the fiberglass pan and the fiberglass outer wall of the Chinook. I filled that with thickened epoxy.
I'll have to look back at my photos now to see about the drainage....
Okay, a few photos. Is yours similar?
First of all, here is the hole after I removed the original water heater. You can just barely see the two improper holes on the "floor" of the pan, they are right up by the front lip. You can also see one of the teensy plywood strips (that accept the fasteners to hold the heater in) drooping down at the top, completely fallen off it's "mush" that sort of held it in place. I think the fact that these strips are so teensy is why they added the holes in the bottom (which Suburban says not to do for obvious reasons).
Here I'm in the process of filling those holes, plus while I was at it I fixed a little void in the layup on one of the chocks at the rear (no big issue, just figured I might as well). What you can't see, because it's behind the front lip, is that I think I also removed some caulking globs and filled some of the pan-to-shell gap.
This is the new water heater set in place but not yet fastened. Obviously you see the gap around the edges, and as you say, water can flow on the bottom edge. I can't at the moment remember exactly how that's sealed, but I think the door/frame has some sort of mating lip. Whether or not that's a great design I can't remember (which I realize is your question!). I think it was a pretty tight fit though?
I believe any leaks would go down into the battery compartment, which does have a drain on the bottom (at least on my year/design). I don't like leaks though, on principle.