I have no idea why MS would choose to mix-and-match. Maybe the margin department has a global limit and that's hit by giving most of it to Musk? Maybe the margin department only covers the amount of Musk's stock they think they can sell in a margin call without causing the stock to tank? Maybe the other loan was using SpaceX stock (margin would only apply to public stock)?

It's also possible that Elon is getting a lower rate for the non-margin loan, but at a much worse multiple (putting up far more shares as collateral).

But that's all making stuff up.