It really comes down to what you want out of your boat and what kind of water you use it on.  If you boat only on glass, you will never have a problem.

A full setback is not for everyone.  If you run hard in the chop, I would recommend against it.

Removing the little bit of fiberglass, where the keel and transom meet, behind the intake combined with the reduction in bonding area allows the hull to flex more.  It doesn't really seem like a lot, but it makes a difference.

This isn't a problem until you are running hard in the chop.  The pounding and torsional flexing of the hull against the rigidity of the intake puts a lot of stress on the epoxy.  It is the flexing characteristics of the dissimilar materials, aluminum against composite, that places the epoxy under shear stress.

In some cases, you don't have a choice.  If you are using a using a Berkeley or clone intake, there is enough vertical clearance, between the bonding flange (behind the shoe) and the suction flange, to not cut the transom.

A low profile intake has no vertical clearance, so the transom needs to be cut out entirely behind the intake, so that it can sit flat.  I think that leaving a small flap of fiberglass behind the shoe is pointless for strength.  In this case, I think it is better to compromise on performance and have the back edge of the shoe out 1-1/2" max.

In the case of this Southwind tunnel, we set the low-profile intake in the best location for performance.  The pod is so long that this is an unusual case.  It isn't really like a typical setting, the back surface had to be trimmed slightly so that only a few inches of the suction flange protruded through.  The fiberglass on the bottom, behind the shoe was left intact.  Overall, this made a very strong installation and this boat works very well.  This is not a rough water boat though.

If you don't mind inspecting for cracks and understand that you might have to reset the intake, maybe it's for you.