There is a certain vendor, and I can't mention their name (B&G), that tries to spec in Top/Top always because they used to be the only major HVAC pump manufacturer to offer top/top configuration, and may still be for all I know. There are arguments for both designs but they really don't amount to much more than marketing gimmicks.
The top/ top does save floor square footage in a tight mechanical room, but really depends on the piping layout if that is an advantage or not. In terms of flanges, there shouldn't be any load on the flanges AT ALL from the piping; they are not pipe hangers, and that goes for the horizontal configuration as well.
Side/side or, splitcase pumps as they are commonly called, are fairly easy to open up for inspection, but as I recall, the bundle comes out fairly easily on the B&G's also (oops, I said their name again). A competent maintenance crew can deal with either pump with no inherent advantages or disadvantages other than their experience with one or the other.
I would not put either design as preferred because you will paint yourself (or the owner) into a corner in terms of having choices. I would be more concerned with efficiencies, NPSH margins, shaft L3/D4 ratios, etc. And the slower a pump runs, the longer it will last.