Beacons are tough. Tougher than you if you get thrown against a rock or a tree or buried under the snow. With that in mind, if things were so bad that there was any concern about my beacon being damaged in an avalanche I would certainly be more worried about whether I could survive the impact. Clothing is not going to provide much shielding against the sort of impact that could damage a beacon.
That brings me to the harness. The biggest risk to the harness is the buckle coming unclipped, breaking, or the straps being severed. Unless the straps were to get caught on something very sharp, high tension alone would not be enough to break the straps. If you wear your harness every day on top of your layers and maybe store it in the sun, then sun bleaching can definitely weaken the harness. I don't know exactly how strong the average harness strap is, but Black Diamond QC labs tested sun-bleached versus shiny new slings and found that while the breaking force was reduced by sun bleaching, the force required to break a sling or cordelette tied into a loop was in excess of 10kN (https://www.blackdiamondequipment.com/en_CA/experience-story?cid=qc-lab-old-vs-new-gear-testing). Considering that you'd be hard-pressed to generate loads like that even when rapelling, it is hard to imagine a scenario where snagging a harness would cause the strap itself to break. Granted, avalanche harness straps are't rated for climbing, so the threshold would be lower.
I postulate that the weak point isn't the strap, it is the buckle. Check out this video in which they test the tensile strength of the sort of strap you'd find on a backpack: https://www.admet.com/outdoor-gear-buckle-and-webbing-breaking-strength-tensile-test/. Notice that the strap breaks at the buckle where the webbing connects. The graph is tough to see, but it looks like the breaking point was just under 100 lbs of tensile force, compared with ~3000lbs for sun-bleached climbing webbing. With that in mind, I'd be most worried about the ability of the buckle on the beacon harness to withstand a dynamic impact in the event of a snag. Make sure you keep that harness snug!
Considering the data, if you were really paranoid about the strength of the beacon harness, you could fashion your own harness with climbing webbing using only knots to close the loop. As long as it fits snugly I'd have no concerns about the integrity of such a harness in an avalanche, whereas I'd be worrying about the buckles on a commercial harness. Just make sure you use appropriate knots because some will slip or reduce the force required to break the webbing/cord.
Overall, I like the reasoning you use in your post: if you have to take the beacon off when you delayer, you're putting yourself at risk by being beacon-free for as long as it takes to delayer. For me that's reason enough to keep my beacon under my layers.