Can I use a section of my thesis to "soap-box" about a meta-issue regarding research?
I think this is a fairly bad idea, for the following reasons:


It's largely shouting in the woods. Let's face it, while you may feel that your thesis is the only piece of work that's "truly yours", it will likely also be the least-read piece of your career. More to the point, your (presumed) target audience (young physicists in other departments) are very unlikely to ever come across your statement. How many PhD dissertations of people you don't know personally have you read to the end?
It has a non-zero chance of annoying somebody in your committee. Again, a physics thesis nowadays is mostly there to appease your committee (as few to none outside of the committee will ever read it), so a section that does not contribute to or actively hurts this goal seems like a bad idea. And I would argue that there is a real danger that somebody in your committee is not thrilled about the unconventional political statement in your thesis, as:
You may be unable to write it in a way that it does not come across as preachy. I think the pure existence of such a section will be perceived preachy, so no matter how you phrase it, it may always be perceived as such.


So if your thesis (and formal papers, obviously) are bad places to communicate your opinion on science politics, how can you communicate these matters? Most people I know with strong opinions on political matters of science (be they about career models for young scientists, open access, reproducibility, ...) tend to primarily communicate their thoughts over various social media (blogs, Twitter, Facebook), with the occasional invited opinion piece on the topic in a journal or magazine editorial. Every now and then, they are also invited to talk about the issues they care about in seminars or as invited speakers in conferences. Presumably, in some cases, they have just been invited in general and have decided on their own that politics is what they are going to talk about. This strategy reaches substantially more people (even if your blog entry never jumps across 100 views, that's probably still more than your thesis will get in the next 50 years), and from a blog or Facebook entry, people expect opinionated content, so there is much less reason to think less of you (unless they vehemently disagree with your opinion, but in this case no way of communicating your thoughts will help).