1.) Cuts that are not easy on a gantry. It would be very difficult to do a tenon on a gantry. You could do one side and then flip the piece. Or maybe you could have a special bed with a void for putting stock in that direction. Either way would be difficult to get just right. With the Shaper and their workstation this is a 60 second operation.
2.) Cuts in the real world. If your stock fits into a gantry, great. But if it doesn't then you're going to have to dismantle the thing to get it into your CNC. With the Shaper I've done inlays on-site, in hardwood floors, kitchen counters, on walls, and on a rough surface picnic table.
3.) Sneaking up on tolerances. Again, if you're batching out a ton of stuff you'll get your tolerances once and everything will be set. But when I use a gantry getting the tolerances just right takes a ton of time. On the Shaper you cut a pocket, test fit, bump the tolerance by a thou or two, recut, and re-fit. This is fast on the Shaper.
4.) Storage space. I don't have a ton of space. I have a small CNC (~15" x 15") for small stuff that I want to batch out, but I work out of my garage. I'd love to drop a 4' x 8' CNC in there, but it isn't going to happen. With the Shaper it all goes into a systainer box and sits on a shelf. When I want to do something big I lay some foam down on the driveway to use as a backer, drop the wood, lay out the tape, and go.
It's crazy pricey. But that's more because it's owned by Festool than any inherent reason. If you're the kind of prosumer who goes for Festool-grade tools then it's probably a decent fit.