The implication that companies use H1-B visas primarily to find candidates willing to work for less (e.g. 70%) of a qualified domestic candidate seems like the underlying loophole we should try to close, not just the "fairness" of allocating which companies and fields deserve to exploit this loophole.
But your post raises a good point that money is an imperfect proxy for "value" -- a company with high profit margins can outbid leaner companies (or nonprofits) for a visa, even if the relative value of that visa to the rich company is not as high as it would have been to the other companies.
Three thoughts in response:
First, this "unfairness" doesn't seem unique to a visa auction. Isn't it already "unfair" that mediocre developers at Google earn more than expert mechanical engineers at Boeing?
Second, assuming H1-B visas lower average salaries in the fields where they're used most, then if this program ends up primarily applying to the highest-paid positions (like mid-level engineers at Google) then this might end up reducing some of the "unfairness" above.
Third, I wonder which scheme (lottery or auction) Boeing and their hypothetical H1-B candidate would prefer themselves. Tech companies already game the system and let other companies fight for scraps so having a more predictable (if expensive) pathway may end up being slightly preferable to all parties.