You'll notice a few things...
HIT, POF, PAC, and KSEW aren't R&D entities. They were originally set up as the military's in-house MRO units, and were, by design, closely tied to the each HQ at a very granular level (operations, planning, etc).
Each of them has been a good MRO entity, but couldn't successfully evolve into an R&D-driven entity. NESCOM is primarily R&D, with now production becoming an increasingly important part of its work. Yet it seems to be approaching the production work the way a giant defence contractor would, like pursuing those projects with scale potential (e.g., munitions) that can keep a factory busy for many years, reuse core inputs for different applications (e.g., the mini turbojet for multiple ALCMs, loitering munitions, target drones, etc), and fully leverage the capacities Pakistan does have (like skill in custom integration work, such as Link-17 or Rabat ESM).
OTOH, the likes of HIT, POF, KSEW and PAC were MRO outfits that were managed like sub-branches in the PA, PN, and PAF. They were all organized to do MRO at a really high level, and can execute nicely in that domain (e.g., M109 rebuild or Saab 2000 repair), but not carry original R&D, do commercial work, etc.
The PN started to break this a little by raising NRDI to take on the R&D work, e.g., the JV with ASFAT A.S for the Jinnah-class frigate. So, basically, NRDI will design the ship, but KSEW will make it based on NRDI's instructions.
HIT has ARDIC, which has (IMO) focused really well on subsystems for armour and specific inputs (e.g., gun barrels and mechanisms for tanks). Yet, HIT isn't capitalizing and scaling this work out as much as it could. But in the long-run, I can see ARDIC and HIT having a similar relationship as NRDI and KSEW.
PAF set up NASTP for the R&D work, but it's currently unproven and bar some partnership with Baykar, hasn't taken on a serious big-ticket project yet. But I do think that time is coming, perhaps via a UCAV.