Thank you all for the advice. Peter, the MkIVs were in fact identical to MkIII (the ones I have repaired and "modded") and they have been sent back to the factory by their request.
So, what hardware do I have? In total, 3 sets of exhausts:
Mk2s, both sides mended after cracking only to a bit later crack again. The thickness of the pipes was better than Mk1s but the welding was very weak (it was polished). I think they are pretty much of no use, an historical artefact for generations to come.
Altered Mk3s, currently being used and apparently sound, but the work made on them was very "rough", I know that form must follow function but ... they're not too pretty.
New Mk5s, requiring some work on the car to intall them as per factory instructions (and I either do as told or they'll be void of warranty).
Now, disregarding the old Mk2s, these are my options:
a) The SBM way - keep the Mk3s running as they are, store the Mk5s for a future need.
b) The Gambalunga way (adapted because I don't have Mk4s to work on) - Do a second intervention on the Mk3s so they can take the same mounts as the Mk5s, do the needed changes to the car (drill a few holes, use the mounting parts provided with the Mk5s) and test them to see how it Works.
c) The deano way - store the Mk3, use the Mk5 as the factory instructed (this means not only installing the new mounts, but also to flash the ECU)
Apparently it is not a portuguese condition that in a group everyone has a diferente opinion to all others!

The funny thing is that in this case all the different options are equally prudent and reasonable, all have sound reasons backing them
TBH, I am leaning towards the "Gambalunga way".
Maybe it is best if I stick with what I have (SBM way) because what I have so far is working, but if I can go one better why not?
However, to go for the new exhausts, as deano suggests, will mean that I can't go back to previous exhausts without altering them. I'm referring to the fact that installing the Mk5s requires drilling the bodywork. Also, to make it in a way that follows entirely the factory instructions requires me to flash the ECU (in this case without even knowing what exactly is being made to it), something I'm not to keen on doing.
So ... here's what I'll probably do: I will drill the holes, install the new mounts, but at the same time I will have work done on the current Mk3 exhausts so they can take the new mounts too (and maybe they'll polish the previous work a bit).
I won't flash the ECU (I do like the brutish nature of the M3W and am afraid to tone it down) and I won't use the new Mk5s until I truly understand if this 3rd mount solution, coupled with the 2nd flexible joint I already have, is enough to make these exhausts last for many thousands of kms more.
And I'll still have the Mk5s in store, in case I need them in the future. It would be a simple swap (while installing them now and storing the Mk3 without changing them would make these obsolete due to the lack of the 3rd mount).
Writing this post was helpful for me, I sort of came to a conclusion while articulating my thoughts. Again thanks all for the advice given, and duly received and considered!