Many sources, such as Bringhurst and other style guides, recommend using text figures everywhere except all-caps text. This would seem reasonable for documents containing a lot of regular text, such as books and novels. But how much does this recommendation hold for documents that contain a lot of math formulae intertwined with text, such as textbooks and scientific reports? Of course, using text figures in math proper is wrong, but what about text figures in text and lining figures in math? Is it better/worse than using lining figures everywhere?
(Posting my comments as an answer, for what it's worth.)
It's mostly a matter of taste. People aren't really used to text figures in math related texts, but it's perfectly OK to use them as long as you do what you already mentioned in your question: Make a strict separation between text and math, and always use lining figures for math, i.e., for both inline and display math. This means in particular that the
$x = 1$ and
Fig.~1 will differ:
You may not like this, but I see no way out of it. Having inline and display math look diffent is much worse.