Having had a combo machine before (Felder) and used a Japanese combo planer jointer, my thought is that of the two main types of jointer/planer machine, the side-by-side type offers certain advantages (chip collection, not having to worry about losing previous settings with the planer when changing between functions), however side by side always means a wider machine than the over/under type of machine. If space is at an absolute premium, then the over/under type would be the route to take.
But if a wider envelope is okay, then one could also look at nesting a separate jointer with a separate planer in the same arrangement - -at least with Martin, where they are designed to nest back to back and offset:
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Of course, that isn't going to be an option for too many people given the sky-high cost.
My current flow between jointer (outfeed) and planer (infeed) involves taking three steps and turning the lumber 90˚ to the left, so it's not too bad.
It's good to have an arrangement of jointer and planer, whether a combo machine or not, that gives a good workflow between operations. Jointing and then maybe a turn left or right to reorient the material, and into the planer it goes, in a smooth flow. It's almost invariably the case that a job that goes over the jointer goes over the planer next. For that, it is far less convenient is a machine where you have to flip tables up, put a dust collection plenum in position, and so forth, to go between functions.
The problem with any machine in which the planer table height is changed when converting the machine back to jointing mode, is that sometimes in a process you have an unfortunate incident in which a stick gets damaged in some phase of fabrication, and you need an extra stick. That means jointing a fresh piece of lumber, but that also means in changing to jointing mode the thickness setting of all the other material run previous is lost (i.e., the sticks you are working with at the time), so you run the risk of having a new part which is slightly out of dimension with the others of its kind. There are workarounds to that of course, but I think design-wise it is at the bottom of my list at least.
My shop is getting cramped for space, but I don't have any inclination to return to a combined jointer/planer machine to ease the situation. Instead, I have built my space around the jointer and planer. I use them in every task with solid wood.
If you can, having separate machines is best in a lot of respects, both for workflow and for having options in terms of how you position the machines relative to one another.