The government bureaucracies prefer this, and have at different times and in different jurisdictions cracked down on whatever other sorts of work-matching arrangements startups have attempted to use, for themselves or as a clearinghouse for others.
The likely threshold for the "compliance issue" could have been that Wallace (the tweetstorm author) had few or no other clients, and was billing this single client full-time hours over a significant period. That full-time exclusivity is a major factor in the tax/regulatory authorities wanting someone to be classified as a salary- or wage-employee.
Now, the very reason that the ultimate client prefers to use Upwork, rather than contract directly, is the headache of complying with these rules. They figure: we might screw up the 1099s, or cross some fuzzy compliance barrier, and then be hit with an enforcement action, if we try to handle our own freelancers. But if we use Upwork, well, they're the experts in ensuring "compliance", and have such a large roster of capable freelancers that neither we nor they would be at risk of appearing to be in an exclusive employment relationship.
Thus: the ultimate villains here are the tax/employment-regulation authorities. They've made the sort of arrangement that both Wallace and the client prefer incur extra legal risks. Upwork has just been clumsy in communicating that, and helping those on its platform navigate the rules.