How to save a dish with an onion paste base which tastes like raw onion paste

Pureeing onions makes them release a lot more of their water than just chopping them, and if you added extra water on top of that, you probably had a very wet paste. That makes it take a lot longer to cook - while you're just boiling away water, it's not hot enough to brown much.

So cook it as long as it takes - it's not going to become bitter. (If anything, it'll get sweeter!) And if you want it to cook faster, don't add extra water. If you watch carefully, you can also turn the stove up hotter at the beginning to boil off water faster, then reduce the heat once it's drying out enough to avoid burning it.

If whatever you used to make the puree doesn't work well without the extra water, you can still use it; just know that it'll make it take longer to cook. Otherwise, you could try grating the whole onion on a cheese grater, which does a surprisingly good job - it'll still be really juicy though!

In order to get crispy-crunchy fried onions, you need to deep-fry them at a high temperature. Pan frying just won't get them crunchy, they'll just get softer and softer as they get browner and browner. I don't know where you are from, but we have a product in the US that is ubiquitous in late fall, particularly on the Thanksgiving table. Perhaps something like this could give an effect more like what you want?

Here's an Amazon search that shows similar products from all over the world.

You say you know that supermarket-spatzle can't be super good, so I am not even going to go there. I'm sure you could find highly rated recipes yourself.

As far as cheese having crunch, the key there is to not stir it while it is getting a bit brown, either under the broiler or on the stovetop (or both, to get crunchy surfaces on both the top and bottom). Also consider using aged Gouda instead of young. That will reach a crunchiness faster, and the flavor will be more intense, allowing you to use less, which will also make it easier to get crunchy.

EDIT: Another thing you can do to get crunchy cheese is to bake it into crisps first, then crunch them up and sprinkle them onto (and into) your completed, or nearly completed, dish. That way you can get melty (with the same cheese baked in) and crunchy if you'd like. That will work with any hard, aged cheese like Parmesan or aged Gouda.

That picture is from Giada De Laurentiis's recipe for Parmesan Crisps.