I don't know myself since I rarely Junker these days but from what Impy has told me Pscrap was kind of bad before this perk, even with the recent changes (RIP original BALANCED Valetta 14k sell point >.>).
Personally, even though the point of a perk is to give benefits to an official faction, I think it's a good thing that Impy is using his perk to benefit his indies as well as the official faction. Imo faction leaders should be looking out for their indies and trying to help them whenever/wherever possible. I feel some official factions not only don't do this, but they refrain and almost distance themselves from their indiebase entirely.
Besides, JM still has a bunch of other perks that give inscentives to join. Even without, the faction itself offers fun group piracy oppertunities that an indie Junker may struggle to find on their own.