The big bugaboo you hear, of course, has to do with the inconvenience of changing from one function to the next. The fact is, as advertised, that the changeovers are done quickly and easily. For example, on many combo machines a single fence functions for both the table saw and jointer, so going from one to the other is as simple as moving the fence. (Mine required an upgrade to get such a fence.) Switching from the jointer to the planer or vice-versa takes a minute or two at most. Setting up the shaper is as simple as bolting the fence onto the table. And setting up the mortiser is the same -- just bolt the unit onto the side of the machine.
Here, O'Malley runs boards through the planer and tablesaw. He put an aftermarket rip fence on the machine, which allows him to leave the standard, double-duty jointer/tablesaw fence on the jointer full-time.
No, the major inconveniences of a combination machine are not the changeovers; they have to do with how being set up for one function limits your ability to use another function at the same time, the way you can with independent machines. For example, when I make several rip cuts from a wide board, I prefer to joint the edge of the remaining board before each rip. (Sometimes the board warps and I have to joint it.) With my combo machine I'm forced to move the fence to the jointer, and then back to the saw, and risk getting cuts of a slightly different width.
With the planer, once I've planed stock to thickness, I must lower the table in order to use the jointer. (Also, in the planer position the jointer tables limit movement around the machine.) So if I find an hour later that I need another piece of stock at the identical thickness, not only do I have to re-set the planer, but I have to get the piece exactly to the same thickness. Similarly, if I'm mortising door parts and make a mistake, I can't replace the part without breaking down the mortiser in order to use the planer.