We are entering into a odd area - I began by stating a distinction between formal mathematical proofs, and matters that can be proven by science. I then added the need for a philosophy of science to examine theories and general treatments in the sciences, and it is in this area that we may have meaningful discussions regarding the nature and robust development of general theories of science.
To now use facts as opposed to proofs is an odd addition to this argument. A fact may be the length of say, a C-H bond; a proof is the clear and unambiguous identification of chemical bonds per se. The theory of chemical bonding has taken a long time to be fully developed, but at no time was the nature of the chemical bond been controversial (unless you go before atoms and molecules were understood) - that is chemical bonds involve electrons shared between atoms to form the various chemical bonds in molecules.
It is nonsense to then consider evolution in the same way. Even proponents of (I would say Darwinian evolution, but even here terms become vague and slippery) evolution admit to its failures and many changes. If you want to use the analogy of chemical bonds for an odd argument for evolution, you would need to show that the idea of electrons forming bonds is vague and often shown to be incorrect. This has never happened. Thus we can accept the nature of chemical bonds to be proven by science. The theoretical treatment of chemical bonds may occur at relatively simple levels, and progress to ab initio QM treatments. These theories are robust and with increasing computing power, have been applied to ever more difficult areas. The maths that is an integral part of these treatments is subject to the same treatment as any other robust theory in science.
So again I add my general comment in this exchange - we have an odd and naĂŻve discussion of proofs in science, and it appears to me, motivated by a need to bolster the semantics of evolution. This smacks of defending an ideology and in the process making science appear murky.