Unfortunately that is by design.
Since Magic Mouse's battery is flat based LiPo battery, if it's used while being charged there's chance of overheating. It might be easier to disippate heat on phones, but not on mouse.
Hence the bottom design to prevent user from using while charging.
Other batteries uses cylindrical battery design.
Hmm. Maximum cooling of a battery depends on a high surface area-to-volume ratio, which is provided by a long skinny rectangle. In two dimensions the
lowest surface area-to-volume is a circle, in three dimensions it's a sphere. That is why commodities which need to be kept cold (liquid ammonia, LPG, milk) are shipped in cylindrical semi-trailers, and certain chemicals at refineries (not sure which chemicals) are stored in spherical tanks, which are rather hard to build.
I've no doubt that the bottom charge port requirement may be due to battery cooling requirements, but it sounds like something else is in play here. Maybe Apple should build a Pro/Ultra mouse with an aluminum body, to match the Mini/Studio,
and provide better cooling. Of course, I'd hate to grab a metal mouse all the time and I'd wrap it in a nylon cover, just like I have my AppleTV remote (which features a convenient deep cutout in the back, perfect for holding some table salt when I'm eating celery in bed watching TV; freeing my navel for other things). 😁
EDIT: Oh, and if anyone else didn't know what "LiPo" was, Siri (without help from ChatGPT! They grow so fast....) told me that it stands for "Lithium-Polymer", just a newer name for "Lithium-Ion". It does not stand for "Lithium-Polonium", something that concerned me as a former nuclear safety engineer.
😛