> To stick with a single example: is it safe to favor customer collaboration over contract negotiation when dealing with high budget projects?
Yes, but note that the client is inside the circle, not an external force, in Agile.
> Changes in requirements, delays, reprioritizing in client's side, those are all things we know that may happen.
Yes, that is specifically what the point deals with, on both sides. Favoring contract negotiation over collaboration is a very poor way of dealing with those things.
(The X over Y statements in the Manifesto are not X instead of Y, but Y must be centered on supporting X; contract negotiation is necessary, but the terms must be framed to support collaboration rather than impede it by being inflexible for the kinds of things that are known to be likely to change over the time of the project development.)
> How are we going to deal with them after you favored customer collaboration, and that collaboration doesn't exist anymore?
If the need for collaboration was centered in contract negotiation, then that will be addressed.
> The biggest problem of Agile is that it takes Trust for granted
The biggest problem (though far from only) problem of Agile is that the authors of the Manifesto underestimated the degree to which people would misread “over” as “instead of”, even given an explicit admonition that that reading was incorrect, making the Manifesto terse and catchy, but ineffective in communicating it's core ideas.