My tilemap rewrite in v0.96 uses a large number of sprites to create each tile for each layer. 1024x576 map uses 34*20*3 sprites, or 2040 sprite objects. And that's just for the tilemap drawing alone--we haven't even touched the windows, events, animations, etc.
There's been a toss up over how many sprites you can have at one time and not lose performance. My Windows 7 can have thousands of sprites and show almost no sign of lag in RMXP. In an RMXPA project, the lag was largely noticeable (FPS of single digits). However, I think it is due to the modified RGSS3 file provided in the package since 5000 sprites created in a RMVXA project didn't slow anything down for me. You need that file in order to create larger resolutions than 640x480 (going any further with an unedited one stretches the graphics). Drago reported his Windows XP lagging a lot, both in RMXP and RMXPA.
v0.93 uses large, map-sized bitmaps. These are handled much better than sprites (you can have thousands and there is no drop in FPS anywhere) but they eat a lot of memory. You are limited to how big your map can be because of this (run Task Manager and see for yourself). You also have to consider that to draw the tilemap, the script uses a lot of Bitmap#blt calls before the map is loaded. Also, to update the animating autotiles, Bitmap#blt must be called frequently. v0.93 has a lot of graphical display errors (you pointed one or two of them actually).
v0.96 (and above) hardly uses any memory and does a series of Sprite#src_rect to draw the tilemap, which is extremely fast compared to Bitmap#blt. You can make 500x500 maps with autotiles galore and have pretty nice performance. It's just larger resolutions are iffy at this point.
The real challenge becomes trying to find a nice balance between Sprites and Bitmaps or having to suck it up and sacrifice something.