There are pros, and cons, to permanently applying PTFs. General rule of
thumb is to permanently apply all PTF's before an OS upgrade. Failure to
do so will leave many orphan objects on your system for all eternity. For
example, let's say ptf SI12345 fixes program QSOMETHING. When you put on
ptf SI12345 IBM backs up the original program QSOMETHING into a save file
and leaves it on your system. This way, if you remove that ptf, it can
restore it from that save file. When you permanently apply SI12345 it
deletes the save file containing the original QSOMETHING. If you've ever
watched your IPL during a PTF apply and saw "5000 objects processed"
during the apply of one ptf, you start to realize how significant these
ptf save files can be.
The main con is, if you want to back one PTF off. It gets to be rather
tough, if it's permanently applied. Normally not something you do if
you've been running that PTF for a few months.
The exception that proves the rule is Domino. I never permanently apply
PTF's to Domino unless I am getting ready to remove that version of
Domino. It is quite often that I have to remove one fix to apply another.
Therefore a Domino shop should probably avoid the APYPTF LICPGM(*ALL)
approach. Do them one by one.