Working on a methodology different from advisor's expertise. How to proceed?
A PhD is a learning experience, so don't worry about stepping out into a new domain. It's also not uncommon for the supervisor to not be familiar with all the research methods you use, since the field has changed a lot since they were engaged in active research.
I understand that this seems daunting, but try to find a support ecosystem where you can get practical tips on day-to-day technical support. There are good resources available online, and very often you are expected to find those out by yourself.
If the supervisor is otherwise good and has a good track record, I suggest you continue with her and give it a shot with an open mind.
Finally, having dabbled in all the areas/tools you mentioned, I have to say I strongly agree with your supervisor, especially from an applied research perspective. In the long run, the effort will probably be well worth it.