That's true, but they still have the amount they were going to pay him over his slot value. For example if they were going to give him 800k they have an extra 450k they didn't expect to have. Or if something coming up in the medical so they lower their offer to Irv to 500k and he takes it because of the medical issue(not likely but possible) they have an extra 300k to spend that they didn't expect to have
They're never going to recover all the lost money when something like that pops up but teams take guys like this late so they'll have something to potentially do with the extra money they didn't expect to have if issues arrive. Obviously that only applies to the overslot guys as not signing a planned underslot guy costs you everything they were going to sign for and more which is why I assumed it was probably a backup plan for Irv Carter if an issue in his medical unexpectedly pops up
Take the 2015 Jays draft as an example, every guy they drafted and signed in rounds 1 to 10 was either at or below slot except Brady Singer who we ended up not signing. It was reported it may have been an issue with the medicals though I don't remember anything being confirmed. Presumably that was done to give Singer overslot by a sizeable margin. They were left with extra cash they could move around(Not the 1.09m for Singers slot but the extra savings from going underslot elsewhere that they were going to pay Singer). They ended up signing Reggie Pruitt in the 24th round to 500k which was 400k overslot(anyone past the 10th round was 100k at the time). They still ended up 435k under the 5% extra threshold. They probably wish they had taken an extra guy to 2 to give Singer's extra money to, though Pruitt didn't work out either, still toiling in AA 6 years later as basically a guy who can run and not do much else. Was that insurance policy worth more than drafting Lance Jones in the 36th round? I guess it depends on how what the likelyhood of something popping up in one of your overslot guys that changes the plan because of course that random 36th round pick college senior might become something too.
https://www.bluebirdbanter.com/2015/6/10/8755563/2015-draft-signing-table
edit: Apparently not signing Bickford in 2013 helped get Tellez as well. Can't remember if that was injury related at all but Bickford wanted more than the Jays offered(which was above slot already), Jays said no and were able to then go way overslot with Rowdy and Jake Brentz(and get the 11th pick in 2014, Max Pentecost, sigh), which wouldn't have been possible if they went much overslot with Bickford. They didn't give Bickford's slot money to them, they lost that, but the underslot money from others which they were saving for Bickford was freed up for elsewhere.