You are all neatly forgetting that even though Trolls had a higher item cost in SR4, it was not enforced at chargen. As a Troll player, I would be massively annoyed by having to pay an additional 50% for ALL items, not just 'ware.
Yes, wired reflexes could potentially need "more" 'ware for a Troll. Yes, the gun would need to be adapted to their hands. But come on, the cyberdeck does NOT necessarily need ANY modification at all, as it could potentially be controlled through VR anyway. And that suprathyroid gland? Who's to say it's any bigger in a Troll compared to a human; for all you troll physiology experts out there, let me know how synaptic nerve endings in a troll brain work, because I have no idea what the size their brains are.
And the above is exactly, to my mind, why it's a good idea for Trolls and Dwarves to just have to pay an increased lifestyle costs; no fuss, no muss.
I play a Troll ganger (a knuckledragger) in SR5; he's got Reaction Enhancers 2, Wired Reflexes 1, and Bone Lacing (Aluminium), for a total of around 80k. At the street level we started at, I not only maxed out the 75K I got from Resources A and spent karma to get the funds needed, I also made do with the 0 special points I got because I had to pick metatype second to even have a CHANCE of affording USED cyberware at chargen. I don't care how much "sense" it makes for Trolls to have to pay more from a setting perspective; I can tell you right now that I'd walk away from the table if a houserule like the above had been proposed, because there is no way in HELL that is fair. Next you'll tell me that because dwarves are small, they should pay LESS for cyberware. How's this for rationale; Trolls don't have to pay more for cyberware because their systems are much more resilient than the other metatypes (reflected by base BOD of 5), and as such 'ware made for trolls are less costly to produce because of the lower quality of raw materials needed. There, solved.
It's already been stated well and clear that Trolls do not pay additional gear costs, only lifestyle. To me, that's the end of the discussion right there.
Now, as for the cyberlimbs; yep, as per RAW you'd have to stat it up from 3 to desired stat. It sucks. Which is probably why you'll see more trolls with muscle toners and augmentations than you will cyberlimbs.
Was this a problem in SR4? You bet, same rule.