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).

The purpose of a thesis is to show that you can do independent research. Your advisor and your committee members will read your thesis to see if you achieved that goal. Anything in the thesis that does not help them determine that, wastes their time (not too much, as they will probably just skip it, but still it risks annoying people whom you don't want to annoy). Lets be honest, those are the only people who are really going to read your thesis. So you can expect virtually no gain from doing so, as you are not going to reach anyone who might be interested in what you have to say about FOSS, and there is a very real potential of harm to your thesis from doing so.

I agree with the other answers that it is a bad idea to include a completely separate 'soap-box' chapter of your thesis which is dedicated to your personal political views of FOSS. The key issue is that you are not adding anything that substantiates your thesis. However, I think that if FOSS has legitimately played a substantial role your research project, then there are ways in which you can communicate your point without jeopardizing the integrity of your thesis.

• Demonstrate the utility: Rather than write an entire chapter, simply demonstrate the utility (point below relevant) of the software in your project. Show your examiners (and any future readers) how you used the software to meet your research goals. 'Do' rather than 'say'.
• Reference the software: If you are using open source R or Python packages, consider giving credit by referencing the FOSS software that you used (e.g. R example, Python example). The benefit here is that you can tactfully demonstrate the usage of the software, and avoid coming across as just "talking the talk".
• Acknowledgements: A simple paragraph in your acknowledgements may give you a sense of fulfilment. Not to suggest it's the norm, but I have read several theses in which the student gives thanks to their God and this has not impacted the success of their work. A FOSS paragraph doesn't seem any less appropriate.

I was faced with a similar issue in my thesis, but concerning reproducible research. After consulting my advisers, we came to the conclusion that the fact my entire thesis was entirely reproducible was more than a mere political statement. In fact, many of my research questions, future directions, and implications were centred around this. The key point here is that it wasn't included as a political statement, but to better communicate the research project.