I’m not sure about Nautilus, but Dolphin gives options to either execute or open it in a text editor (assuming it’s marked executable). .run files have been distributed for a very long time and unfortunately they’re still not recognized correctly by most file managers. A new mime definition could of course solve this by grouping them with AppImages, but I find it unlikely this would ever be adopted in mainstream distros.
The fuse2 vs fuse3 issue is tricky as fuse3 for some reason breaks compatibility, giving the choice between supporting older distros with fuse2 and newer with fuse3, but not both. I could probably use a patched version of fuse like the standard AppImage implementation just started doing, I need to look into it further.
The format is still pretty experimental, my goal currently is getting them to 100% compatibility parity with the standard implementation, which to my knowledge should just be using the patched fuse, then patching the squashfuse binary to allow for extraction without fuse