Back in the good old times, more than a decade before the introduction of Loot 2.0, former Community Manager and Chief Information Officer of MindArk PE AB, Marco Behrmann (the one and only!), several times stated that repair PEDs go straight into MA's pockets, and the costs you mentioned were directly lost to MA with no return.
I think Marcos statement was only partially correct, as I always believed MA takes a certain "cut of everything", consisting of "this and that", with a little less from super-equipped Überplayers and a little more from the losing majority.
With certain gears the old game mechanic allowed steady ROI to be higher than 100% TT value, resulting in guaranteed profit by every shot fired, which steadily shifted PEDs from MA to the few lucky ones owning the gear. To finance their business this forced MA to take an even bigger share from the "losers", just too much to keep them playing and paying.
The losing majority just wasn't willing to tolerate this anymore. The whole system was close to shatter and MA was forced to develop Loot 2.0 game mechanics.
With Loot 2.0 this was shifted more or less completely to the "cut of everything" model.
Nowadays, with very few exceptions MA only feeds from the difference between your personal average return rate (approx. 92-98%) and the aspired 100% TT ROI.
No matter if it feeds from repair costs, ammunition, UA, modified loot return, or whatever sources it can be taken from.
The new game mechanics of Loot 2.0 (PEDs in -> [effective return rate below 100%] -> PEDs out) is the model which guarantees MA a certain profit from player turn over (all PEDs cycled through game mechanics, which includes repairs and excludes markups) and prevents guaranteed return rates above 100% TT value.
The return rate algorithm marginally adjusts the [effective return rate]-part, till it reaches the return rate that MA considers to fit to your gear and style.
Today you can win only by selling your loot with enough markup to cover or overleap your personal gap to the aspired 100% TT ROI.
Concerning your question, with Loot 2.0 your repair PEDs are (re-)injected and just are a part of all your PEDs cycled through game mechanics.
It doesnt matter if your cycled peds consist of 100% decay or 100% ammo or any other combination between the both.
If necessary, your effective return rate ticks up a little, till it meets your assigned return rate in the long run again and the beneficiary of your actions gets ticked down equivalently, so the system keeps in balance.
