I'm answering questions based on the specific question, you're giving generalizations Sure, on a 944 it might be hard to put a DBW pedal in the car. But it's not hard in a Miata, and Poser asked about a Miata.
We do use almost exactly the same parts in each Miata swap, actually. At least, we have after the first couple of cars. This way we only have to solve a problem once and it allows us to offer a more polished final product. We can also do things like have specific parts built for the swap such as our radiators, exhausts and even small brackets - they end up being less expensive and better than one-off fabrications.
Wanna see the list, right down to a $1.95 diode? http://www.flyinmiata.com/V8/costs.php
There has been slight evolution as we go, of course. We've developed an improved intake. The exhaust wasn't used for the first few cars before we got it ready. The bracket for the exhaust was recently redone for more strength based on my experiences with the Targa Miata. And we just did our first swap using a standard LS3 instead of the LS376/480 crate motor, and the improved light throttle driveability will probably make that our engine of choice for the future. But generally, any changes are of an evolutionary sort and not just a "let's make this different" type. Our customers are happy to get a well-tested product, and usually they're prototyped on our own cars first.
We stick with crate engines because we don't want to be responsible for whatever is lurking inside a junkyard one - and because our initial install showed that GM is a lot better at engineering than a lot of aftermarket companies. Every failure we saw on Elvis was directly related to the non-OE parts we put on/in the engine - PS bracket problems, rocker arms, CNC-ported heads that ventilated the water jacket into the intake port. Besides, it's hard to beat a two-year warranty on a 480 hp engine. People don't come to us looking for the cheapest V8 Miata, they come to us looking for the best. For the cheapest, you need to build it yourself. Although crate GM motors are less expensive than you might expect, as they're taking advantage of mass production. The LS3 crate engine could have just as easily ended up in a Corvette. Once an engine goes out of production, the crate engines change.
GM also supplies the PCM and wiring harnesses (and throttle pedals) as part of a supporting package for the engine. The rear diff is brand new. T56 transmissions are getting hard to find new, but we have a small stash of them. The Magnum that's now available is a bulky critter.
My own cars are different, of course. The MG is a one-off. The Targa Miata uses a lot of the standard FM swap parts, but the engine was at the request of a sponsor. The PCM and wiring was a matter of convenience, as we had it in the shop and we weren't willing to use it on a customer car.