No scientific method I'm aware of starts out with: 'Step #1: assume a form of naturalistic uniformitarianism. If you think it does, please cite the reference for that. (I would say that is just a belief you (and many others) hold there).
There's no pre-conditions needed prior to doing science. In fact the one you claim there, makes zero impact on the outcomes of properly conducted objective testing, anyway.
If you think it does; can you give an example of where you think it does?
So too, does the type of mind which perceives those processes and laws. How do you discount that demonstrably evident fact, (along with any of its influences), in forming the conclusions on the constancy of 'processes and laws' there?
Science's 'laws and processes' were evidently distinguished for the purposes of being useful for us. They make sense to a human mind. There is zip objective evidence that they would make sense to non-human minds elsewhere in the universe. (In fact the latter mentioned type of mind there, still takes a human mind to imagine it as existing, anyway ..)
No .. they don't think about them because they are completely irrelevant to the science they're doing. They are therefore not part of doing science.
Your assumption there is nothing more than yet another untestable belief, which is neutralised and bypassed in the drive to perform science's objective testing.
Its also noted that you almost demonstrated why those assumptions have nothing to do with science there .. (which was my point). You however, backed away from forming the logical conclusion there for some reason though ..(?)
Why do you think 'their models don't come up against them'?
I agree that science (in particular, QM) returns knowledge which forces philosophical rethinking about 'what nature is like'. That rethinking however, stands quite independently from doing science. This is the main point I'm making here. Philosophy is not science. Science starts out with no pre-assumptions about the nature of reality. Such pre-assumptions are philosophical notions, as they invariably assume untestable 'truths' (aka: beliefs).