This was cool! I enjoyed a lot of the "fluff" features like achievements and the (seemingly pointless) arachnophobia setting, really shows that you had fun making it. In terms of game design, I have a few notes:
1. When fully upgraded, I enjoyed watching the blocks shoot straight into the hole, but I had to get a really specific angle in order to do that and assist with manually mining. Making a change to the mine (like an "operator chair" or something) so you could watch every block you mine easily would be a great addition.
2. For this sort of "progressive exclusive" currency, you run into the issue of fully upgrading a resource's output and then having almost nothing to spend it on. Having some way for the earlier resources to contribute later into the game (e.g. being able to convert 100 bronze -> 1 silver or each silver upgrade also costs some bronze and every gold upgrade also costs some silver and bronze) would help to make it feel like that effort wasn't wasted.
3. I loved how each universe kept running while you were away, but each universe (apart from Base) was exactly the same, just with a different coloured block. Having different layers like this in an incremental is the perfect time to shake things up a bit with the game loop, and you have even more options with it being in 3D. e.g. Maybe in universe 3 you have to swim with the block, or in universe 4 there are bridges over lava you have to traverse (or maybe silver blocks are actually spheres, gold melts if you leave it too long...). The more usual way is to introduce different ways to get the resource, or add extra steps, which you could also do.
4. If you're interested in making more incrementals, I would steer clear of Unreal in general. A lot of people choose to play incrementals because they don't have very good hardware. Mine's not too bad (i5-12400F, RTX 3060), but having it whir at max speed while I'm trying to watch a YouTube video at the same time isn't a very relaxing experience. You might be better off with Unity rather than Godot (Unity uses C#, Godot can use C#, but not for web builds - I use it because I like GDScript), but it's worth shopping around even if you do go back to Unreal in the end. It's not like there aren't popular 3D incremental games (e.g. Berry Bury Berry), but it'll always be an uphill battle for jams with Unreal.
Blah blah blah. Anyway, I enjoyed it and good job! :)