I find the order (past, present, future) more natural, but I think any order is ok. Choosing a different order puts a slightly different emphasis: if chronological order is not used, then the first time period is the focus of the sentence.

Peu importe ce qu’ils ont fait, font ou feront. → treats all time periods equally, which emphasizes the untimeliness of the claim.
Peu importe ce qu’ils font, ont fait ou feront. → this is about what they habitually do; they started this habit in the past and will continue in the future but the sentence is centered on the present.
Peu importe ce qu’ils feront, ou font ou ont fait. → the sentence is about the future, and anecdotically what they did before that future moment is also unimportant.
Peu importe ce qu’ils ont fait, ou feront ou font. → the sentence is about the past, and anecdotically what they did after that past moment is also unimportant.

(The other two orders are also possible, but sound a bit weirder.)