The way I think about it is that we're already making decisions like this in our own lives. Imagine a teenager who gets a summer job so they can save for a PS5. The teenager is making an implicit moral judgement, with themselves as the only moral patient. They're judging that the negative utility from working the job is lower in magnitude than the positive utility that the PS5 would generate.
If the teenager gets a job offer, but the job only pays minimum wage, they may judge that the disutility for so many hours of work actually exceeds the positive utility from the PS5. There seems to be a capability to estimate the disutility from a single hour of work, and multiply it across all the hours which will be required to save enough.
It would be plausible for the teenager to argue that the disutility from the job exceeds the utility from the PS5, or vice versa. But I doubt many teenagers would tell you "I can't figure out if I want to get a job, because the utilities simply aren't comparable!" Incomparability just doesn't seem to be an issue in practice for people making decisions about their own lives.
Here's another thought experiment. Imagine you get laid off from your job. Times are tough, and your budget is tight. Christmas is coming up. You have two children and a pet. You could get a fancy present for Child A, or a fancy present for Child B, but not both. If you do buy a fancy present, the only way to make room in the budget is to switch to a less tasty food brand for your pet.
This might be a tough decision if the utilities are really close. But if you think your children will mostly ignore their presents in order to play on their phones, and your pet gets incredibly excited every time you feed them the more expensive food brand, I doubt you'll hesitate on the basis of cross-species incomparability.
I would argue that the shrimp situation sits closer to these sort of every-day "common sense" utility judgments than an exotic limiting case such as torture vs dust specks. I'm not sure dust specks have any negative utility at all, actually. Maybe they're even positive utility, if they trigger a blink which is infinitesimally pleasant. If I change it from specks to bee stings, it seems more intuitive that there's some astronomically large number of bee stings such that torture would be preferable.
It's also not clear to me what I should do when my intuitions and mathematical common sense come into conflict. As you suggest, maybe if I spent more time really trying to wrap my head around how astronomically large a number can get, my intuition would line up better with math.
Here's a question on the incomparability of excruciating pain. Back to the "moral judgements for oneself" theme... How many people would agree to get branded with a hot branding iron in exchange for a billion dollars? I'll bet at least a few would agree.