You do get stronger because the weapon trait unlocks are permanent and the unlocked items get permanently added to the pool available during your next run, you also unlock a new gadget after Ixion in Biome 2 and you'll get shortcuts between Biomes and a hard checkpoint after 3.
It's just more subtle and RNG-dependent and why it's like that I have no idea, I haven't even completed it yet due to leaving it after I'm done with other games so I can focus on it, reached the end of Biome 3.
Basically the entire game is like a planned run through Biomes where you try to get as strong and play as consistently as possible to be ready for the bosses, no other way around that and I understand it might not be everyone's cup of tea.
Hell, it might not even be mine when I get back to it but it is what it is, enjoyed the reruns so far and definitely felt like I myself was getting better on top of unlocked weapon traits and other stuff.