Golden rule of doing PhD studies:
Don't argue with your supervisor*
- They are much more likely to be right than you are, simply because they've been around much longer than you have.
- They likely want the best for you. It's possible they want the best for themselves even more, but because students doing well also reflects well on the supervisor, your motives overlap.
- If your relationship with your supervisor breaks down, you suffer a lot more than they do.
- They could have other, non-obvious reasons for wanting to submit to high IF journals (such as needing it for their upcoming tenure review or funding application).
So if your supervisor selects journal based on impact factor, you submit your papers to those journals. Worst thing that can happen is your paper gets desk rejected, which is still not a terrible outcome because you can submit it elsewhere. The only practical consequence is that it takes a bit longer to publish, but if you've uploaded a preprint somewhere, actual publication in a journal isn't a big deal. Your results are already available, after all. Meanwhile, there is no benefit to publishing in a low-IF journal compared to a high-IF one.
If you really feel strongly about it you could try negotiating with your supervisor, something like "how about we send two manuscripts to high IF journals and one to low IF journals". But if your supervisor digs in his or her heels and insists you submit to high IF journals, see the bolded sentence above: don't argue with your supervisor.
*Unless they are doing something unethical.