While they could trade everything to thier main account, I suspect most people who multi-acct do form emotional attachments to their multiples.
I also suspect most people who multi-account do it for raiding, and to prop up raid numbers to necessary levels in their area. In which case they wouldn't want to drain that account of pokemon it needs to raid.
Trading might have flaws, and I do understand your concern but I think it's overexaggerated and not really that big of a deal to prevent trading for that reason.
((Spoofers and Selling is a completely different topic))