@bgillisp Fair point, but I'm not sure I'm 100% sold.
This doesn't directly address this post, but I do want to take a stab at defending the concept of large map counts rather than simply letting the answer to the request be: "Why the crap would you make that many maps?" I'm not familiar with the game in question this is being compared to, but I will address another game that involves some puzzles.
Let's take Legend of Zelda, which is an action/puzzle RPG (not really an RPG, but in the loosest definition you could call it one... Certainly you could build it with RM).
The overworld had 19x8 maps, so ~150 maps there. Each map (just a quick count) was 16x10 tiles.
There were 9 dungeons, each with two sets of maps (for 1st and 2nd quest). Each dungeon appeared to have around 18 maps (some more, and I didn't see any less, but we'll average at 18). That gives us 324 maps + 152 = 476 maps.
The game is not terribly complex, and while it may be tedious to make 476 maps, with RPG-maker it doesn't have to be years of work to make it, especially if you have a lot of time to do it. The maps are fairly simple.
Let's say this game has smaller maps (9x9), but twice as many, because the puzzles are being emphasized over combat, and we are wandering through these dungeons. That could easily get us to the 800+ range. While that still isn't greater than 999, it's pretty close.
Is it ambitious? Maybe. Probably. Could the maps be combined onto the same map sheet? Also probably. But I don't think it's unrealistic to assume there are a large number of maps.