Just curious, what made you continue playing the game despite the slog you went through after the early game?
Due to the "Dimensional Remnants" teasing its future unlock on the right-hand side of the universe list I knew there was more content to discover but dreaded repeating a near-identical experience to the previous several hours multiple times to get there. I looked through the game images on the center-right side of the game's itch.io page to see what content I would be missing if I called it quits. The last image has some of the equations from "Modify formulas" and my mind flashed back to an old Flash-based incremental game that I did enjoy playing to completion: Learn to Fly 3.
In that game you were a penguin trying to reach the moon by building elaborate rocketry. It delivered new content through the core gameplay loop (which lasted just a minute or two) by having each iteration reward you with currency used to purchase better parts, which in turn interacted with the environment and the player differently. After the game was beaten there was a New-Game-Plus currency which, like your Dimensional Remnants, altered the equations. I had sunk nearly 100 hours into that game, well beyond its 10 hour single playthrough-time, because I enjoyed the core loop enough to do it one more time and see how much the gameplay had changed. I noticed that the obstacles which the player would struggle to avoid in their first playthrough became practically unnoticeable as you smashed through them with ease after a few wise New-Game-Plus purchases, and there was this feeling of having mastered or overcome a meta-challenge the game was posing: Trivialize the things that were an issue for you earlier. Another good example is in the first Dark Souls, where a demon is a major boss early on in the game, then a standard unit later in the game, and the player gets a feeling of having grown so strong that this previous titan is now beneath them.
Before shutting down Helixteus 3 for good I played just a little bit more into the second universe... just enough to see that, instead of delving into caves, I could simply use a pickaxe and dig deep enough to find a minimal amount of the material required to progress then purchase as much of that material as I needed using dollars - completely skipping over the cave mechanic like it was the obstacles in Learn to Fly 3. I looked back at the image of the equations that the Dimension Remnants could alter, realizing that even if the content was completely identical my power-level relative to the content could change rapidly, and there was a feeling of accomplishment after having "cleared" or "broken" what was a challenge in the previous iteration with ease. I might be able to "break" other mechanics using the equations, I thought, and that promise kept me going though the rest of the early game.
(Granted that promise was eventually rewarded, but I had no way of knowing whether it would be possible in the end-game back when I decided to continue soldiering on.)