I align after to cut out a rotation. Except E perms. I don't know, for E Perms I always align, rotate, and then do the alg. But I voted the second option, because E Perms are only 1/21 PLLs.
I just rotate top layer to whatever is needed to do the LL. Like if I have the bar on the right for an A perm I'll do a U' then do the alg then rotate the top layer to whatever it needs to go to. I don't like have to orient before the pll because then I'll have to rotate the cube to get it to proper position for my alg execution. And imo, cube rotations are something slow that aren't needed at all in the LL.
some alg i dont recognize until i have it aligned, like E and Y i get confused (when its not aligned). so, it has become habit, since i rotate for E much like everyone else, that i rotate for Y, . . . sometimes. i rotate for G perms, and i confuse sometimes with R perms (when its not aligned), so i rotate R perms, . . . sometimes.
so, my answer, . . .
. . . sometimes . . .
E is the only one I've ever aligned. I learned all the PLL's about 8 months ago and aligning the colors never came to my mind as a way of recognizing them. E is the only one that would confuse me, 'cause I use to think maybe I missed something and look over the cube twice. Now it is easy to recognize, but I still need to align it.
I align the PLL to where I solve it, and then align the colors afterward.
If the colors are aligned beforehand, I rotate and solve rather than AUF before and after (though that is easily faster...).
If the U face stays on top during my PLL I AUF last. For all others (for me it's: A, A', F and V) I AUF first. Ns are a special case as its easy to AUF after a z rotation - just a R move.
it really does depend. for algs that end in U or U', i wont auf because i end up doing that after the alg. HOwever, my regoc for G perms SUCKS, so i always have to auf the 2x1 block before, and then auf after the alg