Hi Gonçalo,
I have limited familiarity with the situation with Wikimedia Portugal, but I am glad that there seems to be some movement on a path forward here.
I have had similar questions about WMF trademarks in the past. My quick read of the trademark provisions that you included in your email is that they may need clarification but I don't think of them as being "red flags" that should stop progress.
I don't know what WMF's legal research has revealed regarding WMPT's situation. My guess is that WMF is being understandably cautious about WMPT until WMF has greater certainty about WMPT's governance. You could ask WMF to explain why it made the proposal that it did.
I understand the concern about annual governance reviews. I would support WMF providing sufficient (not lavish, but sufficient) grant funding for WMPT to hire a contractor to perform the governance reviews that WMF wants.
Overall, I think that your concerns and questions are good and should be discussed between WMPT, WMF Legal, and Affcom. I understand why you would make these questions public and request input from the wider community. Personally, I do not see "red flags" in the language that you quoted, and I am glad to see that there seems to be some positive steps happening with regards to the situation between WMPT, WMF, and Affcom. WMPT might consider asking WMF for more favorable terms for the chapter agreement after a period of time, perhaps six months to a few years, if WMPT seems to be progressing in a good direction over that longer period of time. In the time between now and January 31, I think that you are asking good questions but I would not consider these issues to be "red flags" in the short term.
Best wishes,