Fair point. I don't have an ST1100, so I was speaking in general terms (and reading into Factory Pro's bald statement about them). Perhaps the orientation of the ST's V4 engine is better suited to PAIR plumbing, but I can assure you that the same is not the case with Honda's other V4s. I don't think the system makes much of a difference to perfomance or the environment, so leaving it or removing it is really best left up to whoever is inclined to do the work to remove it, or work around it, as necessary.
TBH, if I'm not working on the engine, I leave it in place. But, one of my VFRs has had so much engine work done, there is no way leaving it in place would have made sense. Another bike has a supercharger kit installed, which necessitated the removal of the PAIR system entirely (it was engineered to work without it), and some of the others have had their engines out and re-bored, so blocking off the PAIR and vacuum ports made more sense than attempting to re-install the spaghetti-like componentry. FWIW, assuming the PO hasn't already removed it from my ST1300 (I've never noticed), I have no intention of removing it from that bike--unless and until I start doing work on the engine.
Ciao,