I'm sure a company like MS, who've had traumatic run-ins with the DOJ in the past, has internalized this phony management persona even more than most. And I do believe low-level developers who work on the individual clients are probably 100% earnest. They usually are. It's the people in the political structure who set their priorities and schedules and use them as pawns that you have to worry about.
Even if your postulation is exactly accurate, MS still bears responsibility for crippling the Linux client, no matter which specific employee the communication "fault" falls on.
I have no inside knowledge of Microsoft, this is just generic commentary and extrapolation on corporate politics in general. It is possible that I'm incorrect and this is truly an honest mistake. If this gets any attention, management will certainly claim that, and we'll never know the reality of whether it was unintentional or whether "The Linux client supports those speedups" was intentionally swallowed by someone along the line (or whether the patch was delayed for additional review because it was "accidentally bundled" with a bigger branch, or whether the priority has just been "innocently" pushed down, or whether the team is "just understaffed", or...).
The proof is in the pudding with corporate politics. Being in management is being a professional politician. That's always true. They're always going to try to tell people what they want to hear and cloud up the picture around things that that person doesn't want to hear. If Microsoft is continually engaging in a series of accidents that hurt non-Windows clients, that pattern is sufficient proof of management's intent, regardless of what they claim.
Not knowing the code behind it, but knowing the history of the OneDrive for Business client, I could see a few ways this could happen. The OD4B client has gone through a bunch of iterations before being merged with the regular (public) OneDrive client, so along the way, there could have been optimizations added on that were only available to the new merged client. Due to constraints, this could have been done using a simple UA check. These optimizations could have been merged down to the OSX/Linux clients (not sure if they're using a merged one there, or still the separate ones) but since different teams work on the clients (most likely different teams on each client) and server, the Linux client team never told the server team that the it also supports these optimizations.
Easily could see the above scenario happening, it's not completely crazy when talking about big companies that teams don't have the best insight into eachother's work.
Disclaimer: Work on Microsoft. Not on Windows, not on OneDrive, completely different part of the company.