The pipe you will see in the roof are the feed and supply lines from the "tinacom" and the drains at the perimeter assuming that it is a flat roof. This is pretty much a standard. There should be no structural issues for such a little amount of pipe, after all 4-5" concrete with rebar is fairly strong - much stronger than typical wooden roofs.
OK, so it is a THRU pipe, not some plumbing running in the roof. No structural issue there, most likely (depending on how they made the hole, if it was done "after market").
The only way to cure infiltration there
permanently is to re-run that pipe AROUND the roof line into the house wall underneath it and close the hole with cement/synthetic a mix available at pool supply stores. Water will, thru capillary action will, over time always see its way in between even apparently tightly held PCV pipes and concrete and then by transpirational effect pull INTO the the concrete and eventually again swat out where it's easiest (lifting the interior paint). There is no bonding agent which would be known to chemically permanently bond PVC and concrete.
I know it is quite
standard here to "just" to connect Tinacos thru the roof, Chip (
to no te preocupe, que no pasa na'a... :cheeky:). It is also, to locals at least, nothing but "standard" to have infiltrations here and there and see some water inside the house for the sole reason that it's raining outside. It's also pretty much an accepted standard here to see fairly recent paint chip off again and again or to repaint extensive spots here and there, because of humidity.
I for one, like to think that if one wants an other, preferably better result, one has to do things differently than what is considered standard/bad or questionable result here.
Taking the laws of physics into account, instead of trying to prove them wrong would seem an interesting alternative at least.
Anyways, again I don't know JR's home... it's only start to paint a more clear picture thru these posts. I wished I could have been of more help at once.
... J-D.