Two aspects are important to keep in mind for a decision of this kind:

This machine is going to be your primary professional tool for the next several years - do you really care about a few hundred dollars extra? Especially if you have niche-requirements (read: non mass-market) like strong Linux desktop support and deep concern for privacy / security?

Sure - you could do the research and build yourself and pay less for the parts - but if you consider your time at market rates, are you really making a financially smart decision by not paying a small premium on the price of constituent parts?

Of course, I am aware of the excitement that can be associated with creating a custom build - if you are into that sort of thing: enjoy it as a hobby project, not because it is a better deal.

Humans seem to have a hard time taking costs into account that are not easily quantified.