At GVA they can be a bit tough, I must admit, and I can see this left the OP very unhappy. In a way they don't need to worry too much at GVA, they have some of the largest CE cabins in the network, which makes life easier for all concerned.

The only time I've seen this happen at GVA was when the traveller had 2 bags or more. So if the OP only had the one bag, the small crumb of comfort I can offer is that it is unlikely to happen again, since the SOP is that the bag with the yellow tag is "guaranteed" to go in to the cabin, whereas the larger bag is not. I've never seen someone with a single bag get pinged, so long as it looks vaguely within the size limits. I have a large bag, which is just inside the size limits when the bag is full. It has never been pinged, but it's a shoulder bag, not on wheels, which seems to make it invisible.

If the bag could technically fit under the seat in front, I wonder if readily agreeing / suggesting that would have helped? (Totally unnecessary in most of CE due to the middle seat),

The other point is that because GVA is on FLY, they probably can only ping the first few passengers, since any last minute changes - including offloading - seems to cause nightmares, so while I wouldn't say it is acceptable, I use that as an explanation.