Mordeth_Kai: My memory is a bit fuzzy so I could be wrong, but I think in one of the older builds (a year or two ago) it was possible. Either way, this is the biggest reason I focus on getting money before everything else and go straight for top tier for everything when starting fresh. 500+ nanites for the rng upgrades is a real kicker if you maxed something, as a ship can easily have over 10k nanites worth of upgrades, and a high slot multi-tool can get close.
If the devs really want us to upgrade incrementally they'd fix this.
Beyond did substantially increase the Nanite rewards for repairing Damaged Machinery, extraction from any wall mounted device and terminals in Abandoned Buildings. Also, now that I get hints for where to look for Fauna to scan, for the first time ever I reached 10 in Planetary Zoology, since I was able to scan 100%, which adds substantially to my Nanite budget.
It is still a grind, but in Beyond, I now routinely walk away from planets with > 600 Nanites more in my pocket even without scanning Fauna to 100%, and sometimes even some S-Class Upgrade Modules from Damaged Machinery.
The key to me is having a properly outfitted Exo and a ship with low launch fuel requirements.
I am using the Pilgrim with 3 S-Class Exocraft Engine Upgrades, since it seems to be the fastest of all Exos, and an Explorer with Efficient Thrusters (= 12.5% fuel cost per launch) and the Launch System Recharger.
Edit: Pre-Beyond I'd simply buy loads of Platinum and refine that into Nanites. Now I'm bumping around on planets for that, since it's now actually worth it.
Edit2: And I totally forgot about the Upgrade Modules having their stats determined by order of installation. HG would have to give up on that dumb and half-ar*ed progression-killer mechanic, if you could move Upgrade Modules back and forth between inventories of different ships / MTs, unless they kept some kind of history on the modules ... *sigh*