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.