Your main focus should be on getting results. If tool A can help you get results that you can’t get using tool B, then there is no question that the scientifically correct thing to do is to use tool A. It is literally your duty as a scientist to use the tool that you think is the correct one that’s adapted to your project and that will maximize the scientific value of your work. To bend to your advisor’s will on this seems to largely defeat the purpose of doing a PhD in the first place. Even if it leads you to a marginally more successful academic career, it will turn you into a cynical academic who believes that everything academics do is motivated by self-interest and pandering to people in positions of power rather than a desire to do good science.
However, it is also the case that…
a legitimate secondary goal is to keep your advisor happy. We live in the real world, not a Socratic utopia. In the real world, you are doing your work within the confines of academia, where it is expected that you will not just pursue scientific Truth but also show the ability to work as part of a team, and the humility and tact to defer to the wisdom and experience of your superiors (even on some occasions when they may not be quite as wise as they think they are).
The conclusion is that, in pursuit of this secondary goal, it would not be a betrayal of your principles to spend at least a modest amount of time doing things your advisor wants you to do even if you don’t want to do them or they seem pointless.* So I’d suggest that, in addition to using the scientifically correct tool you’ve identified, you also learn to work with your advisor’s software and try to incorporate some use of it into your thesis and/or papers, to the extent that that can be justified as supporting the science you are doing, even if only marginally so.
* Assuming your advisor isn’t asking you to do something that’s outright fraudulent or crackpotty, that is.
Finally, keep in mind that…
another legitimate secondary goal of a PhD is to learn useful skills. You may not think that your PhD should involve coding, but if you look at it a different way, your advisor is actually giving you a valuable opportunity to acquire some extremely useful and marketable coding skills. When I meet people from industry they tell me things like that software engineers are so much in demand these days that they “can write their own paychecks” (literally a phrase I heard from a senior HR manager at a large Silicon Valley company). So don’t underestimate the value of acquiring coding skills even if they don’t have a direct relevance to (your own personal vision of) what your PhD is about, or if acquiring these skills requires you to get out of your comfort zone. Indeed, it is precisely the things that take us out of our comfort zones that help us develop and grow as academics, researchers, or future [fill in the blank]’s.