I think it's more complicated than that. Downloading 50Mb at the start of the game is ok if you're on a PC with a reasonably fast internet connection. If you're on a cell phone (which usually has a slower connection), and you have to pay for the amount of data you download, it becomes problematic.
If you expand the game over time and it becomes significantly larger than 50mb, it will take too long to load on a PC too.
If you don't use spritesheets (as RPG maker does in some cases) and don't put thematically similar graphics in sheets, this increases the number of files significantly.
In my opinion, it is difficult to find a sensible solution for what is allowed and what is not. That's why I asked support how strict the 1000 files rule is. The answer was that exceptions to the rule are really exceptions.
As soon as the game reaches a certain size and you have a version 1.0, you should make it downloadable and installable.