I'm sorry to hear that, I've heard this happens a lot unfortunately.
Some people have said this plugin helped: https://felesmachina.itch.io/rigodotify
I'm not sure if it still works but I don't have much experience in Godot so I can't help as much as I'd like. Though for the future if you are planning on really doing game dev I HIGHLY recommend buying Auto Rig Pro. It's $50 but I use it more than any other plugin and you can literally rig a character in seconds with it.
I also found this thread on reddit, but again not sure how much it will help: https://www.reddit.com/r/godot/comments/126b28p/has_anyone_had_issues_importing_...
Viewing post in PSX Rigged Character Bases comments
Oh! Haha I was replying above and didn't even see you were already mentioning my Blender plugin. So my plugin basically converts the rigify rig into a Game Dev skeleton. It's not a Godot thing, it's a blender thing. But it makes the rigify rig retarget and IK compatible for Godot, Unreal and Unity. So you get a Game Dev standard skeleton, but with all the benefits of the rigify style control rig in blender.
It'd probably help out a lot of your users if you used it on your models. I know this sounds like self-advertising, and that's lame, but seriously a standard Game Dev skeleton, and you're already using rigify for your rig, so it'd be very minimal difference for you, but it become a lot more compatible for anybody else using the different engines.