Basically, can you spend a navigate token, and stay at the same speed for Engine Tech shenanigans? The rule says spend to raise or lower by 1 and remembering "do what it says, not what it doesn't say" nowhere can I find "you may ignore the effects of your spent token" a token always has an effect, yes?

Yes. This was covered in the FAQ

Must have been using an older FAQ thanks.

Page 1 of the FAQ.

Commands, p.4

This entry should include the following bullet point:

“A ship can resolve a command and choose not to produce its effect. It still counts as resolving that command, such as for the purpose of triggering upgrade cards.”