Thunderbird

Yes, you are right. It says ANY modification/changes requires written permission to use their trademark. This is from their trademark site:

Modifications

If you're taking full advantage of the open-source nature of Mozilla's products and making significant functional changes, you may not redistribute the fruits of your labor under any Mozilla trademark, without Mozilla's prior written consent. For example, if the product you've modified is Firefox, you may not use Mozilla or Firefox, in whole or in part, in its name. Also, it would be inappropriate for you to say "based on Mozilla Firefox". Instead, in the interest of complete accuracy, you could describe your executables as "based on Mozilla technology", or "incorporating Mozilla source code." In addition, you may want to read the discussion on the "Powered by Mozilla" logo.

In addition, if you compile a modified version, as discussed above, with branding enabled (the default in our source code is branding disabled), you will require Mozilla's prior written permission. If it's not the unmodified installer package from www.mozilla.com, and you want to use our trademark(s), our review and approval of your modifications is required. You also must change the name of the executable so as to reduce the chance that a user of the modified software will be misled into believing it to be a native Mozilla product.

Again, any modification to the Mozilla product, including adding to, modifying in any way, or deleting content from the files included with an installer, file location changes, added code, modification of any source files including additions and deletions, etc., will require our permission if you want to use the Mozilla Marks. If you have any doubt, just ask us at name at domain.

Any reason why Thunderbird's version in Trisquel's dagda repository is 3.1.16, when the latest version is 9.0.1 ? I understand that we cannot provide the latest version of each software, but Thunderbird/Firefox seems to be a special case (Trisquel already provides the latest version of Abrowser: 9.0.1).

You are confusing issues. The issue with Thunderbird is a trademark issue not a software freedom issue. The issue with chromium is a free software issue.

If you look at this copyright file provided by Ubuntu there are many files in there with unknown copyright. These potentially make the browser non-free. Those are exactly what potentially makes it a violator.

You can use, study, modify and redistribute Mozilla's products. It is 100% Free software but recommends non-free software. That is why Trisquel maintains its own version without this problem.

The trademark restriction tells that modified versions of Mozilla's applications cannot bear the same name as the original ones. It is perfectly fine. It is only enforcing the trademark so that Mozilla's products can be properly identified (the whole objective of the trademark law). The same kind of restriction applies if you want to sell Mozilla's application, i.e., you must rename them. As Brett Smith says, this looks abusive. I wonder what qualifies as selling though. You can buy many magazines with Firefox or Thunderbird included on the CD that goes with it and, AFAIK, Mozilla has never complained about that.

I have seen the link you posted. The thing is the chromium licensing is a mess. I'm not super good with legal stuff so I can't say which of those licenses is a problem or not (aside from the ones that are obviously free software) but some are not listed on the FSF license page and I can't tell you which ones will be problems or not.

The real problem is because the licensing is all over the place no one has really taken the time to verify that everything is free software. It quite possibly is but we assume it isn't until someone actually takes the time to go through and verify it. Basically we do the opposite of the courts. It is presumed guilty (proprietary) until proven otherwise (free). So until someone actually takes the time and proves it's free we will assume it isn't because of how messy it is.