So, you're capable of JS and web development in particular, and for whatever reason want your game to be transparent, put some, I dunno, pngs of cheese at the background (and for whatever reason map parallax background is not what you want).
This rather small plugin removes permanent black background of the game canvas, switching it to the transparent, so you can draw anything behind your game behind already transparent tiles.
Most likely it won't cause any plugin incompatibility or other weird bugs, but just in case put it somewhere at the beginning of plugin list. Drawing on the background itself is up to the end developer, plugin doesn't have any way to manipulate page background. Never tested with battle scenes (should work) and MZ (may work). Direct background manipulation of body element doesn't work in fullscreen mode (no idea why), you have to create new HTML node.
Plugin itself is in attachments, example project here.
Use anywhere you want, including commercial projects.