They pass through the upper pan ... so no worries.

all but two pass through the pan
 

There are two bolts that do not pass up through the lip of the pan - they are on the rear side (as opposed to the crank pully / front side). These are the two bolts you definately want to torque to spec and not snap off (it would be extra had to extract / retap). I was sure to blast the holes out with carb cleaner to be sure the threads were not full of grit.

There is one extra long bolt (at least on the 126) on the driver's side that has a spacer and a loop that holds the transmission cooler line to the side of the engine before it travels to the cooler itself (transitions from a hard line to a flex line)

Maybe this weeked if I can get some time I'll post pics.
I did a new oil pick up strainer with the pan off, the Dave Morrison check valve procedure, and the oil drain tube (some tips to pass along on this PITA job).

So far so good - absolutely dry. I wonder if I can go with just a "dry" gasket now that I have a new pan. I might give it a shot next oil change.

Hmmm either my memory is slipping or mine is tapped all the way through (on the TD anyway which was retrofitted with a turbo engine). I'll be under her today and have a look.

Also it has spacers on both sides and an A/C bracket that mounts to the pan (nuts on top of bracket).

In any event a shot of something in the hole (I like WD40 as a general product) will cause any grime to pour out.