I don't have anything to say about the drama with PrivacyTools et al. but as a free software supporter I can say confidently that Privacy Guides (along with allied projects such as GrapheneOS, PrivSec, and Accrescent) represent a sect of the privacy community that is at best ambivalent, and at worst actively hostile, towards the free software movement. Their usage/endorsement of proprietary tools can only be seen as hypocrisy if you hold that privacy and freedom are closely linked; the free software community (which significantly overlaps with the privacy community) of course does, and this was common knowledge once upon a time (as the reddit /r/privacy wiki states) but Privacy Guides et al. is more interested in security even at the expense of freedom, going as far as to spread FUD about free software projects such as F-Droid and Linux-libre and about the free software movement in general.

I've written before on reddit about why I feel praising the security of proprietary software is misguided; I'll reproduce that post below:

Privacy guides is not a free software advocacy organization and in fact is not a friend of the free software movement at all, which is apparent when you read about how they praise proprietary operating systems for their security while neglecting to mention the fact that, for proprietary software, "security" often means security against the user.

I've written before about why F-Droid is important here. Their inclusion policy ensures that what I get from them meets the free software definition and thus I can exercise the four freedoms (to run, share, modify, and share modified versions) with it. There is no such guarantee if you get prebuilt packages from the developer, because unless the build is reproducible there is no way to verify for yourself that the source code is complete and corresponds to the binary, and even if it does it may include proprietary libraries. F-Droid publishes the complete source code along with build metadata and instructions to allow users to exercise the four freedoms with every app. Personally I think getting updates a day or two late is an acceptable tradeoff. Free software is even more important now.

Desktop GNU/Linux distributions follow the same model and have an important role in being a third-party curator and distributor of packages.

As others have said, free software is not inherently more secure (or bug-free, etc), but it was never promised to be. Free software only guarantees its users the four freedoms. Privacy guides is a privacy advocacy organization, not a software freedom advocacy organization. They are not the same thing and the fact that people conflate these two movements/communities causes a lot of problems here. Every time someone comes to this subreddit and insists you don't really need software freedom, I think they got that notion from privacy guides or some other privacy community.

As well as a follow up comment:

Sure. I didn't mean to imply security was bad or undesirable. You need security. My point is that, if the operating system is proprietary, the developer/vendor holds the keys and secures the OS against its own user. DRM is the obvious use case for this, but we can see OS vendors abusing this even more overtly - remember that fiasco from last year where Microsoft forced users to open certain links in Edge, and blocked users' attempts at forcing Windows to respect their preferred browser setting.

There was a genuine concern, back when UEFI Secure Boot was introduced, that Microsoft would use its power to prevent vendors from selling unlocked PC's. Fortunately Microsoft decided not to do this, but (from what I know) did do so with ARM devices. We've since come to accept that with non-desktop "smart" devices that this is the norm. That frightens me. It frightens me even more when privacy organizations uncritically praise user-hostile security features and people in "FOSS" communities parrot the advice and opinions of organizations that don't consider software freedom and user control of their hardware as a factor.

(Keep in mind this is from the perspective of a free software supporter, not a security zealot)