Mathematicians also occasionally build on top of unproven foundations (e.g. all popular asymmetric encryption schemes are built on top the assumption that certain problems such as integer factoring are hard, for which there is no formal proof), or at least explore both possibilities for statements with unknown truth value (e.g. you can find lots of work that explores the consequences of P = NP and/or P != NP).
However, there is a major separation between math and programs that I think mostly invalidates your proposal - most math we're talking about here is simply not applicable directly to the real world in any way. It's only studied for the interest of mathematicians. There is no real world consequence for Fermat's last theorem, for example - it was just a really interesting to prove theorem. In directly applied math, such as engineering, it is in fact much more common to work with unproven but well tested conjectures.
What specific areas were you thinking off? I don't recall, e.g., in numerics that things were often just unproven/conjectures, but might be subject matter specific.
Edit: one better example from modern physics - the path integral formulation, used in both string theory and other areas of QM/QFT, is not fully formalized and formally proven to work. Also, a more concrete example of a widely used but actually still unproven conjecture in string theory is the famous AdS/CFT correspondence.
The part of Newton's theory that was troublesome is his fluxions don't have the Archimedian property. It took until the 1960s before Newton's notion of fluxions became rigorously formalized with Non-standard analysis. https://en.wikipedia.org/wiki/Nonstandard_analysis