Increase job tiemout of some flatpak runners

Certain projects, mainly gnome-builder but also sometimes boxes, sometimes timeout during compiling if the runner happens to have an above average load or the timeout is the default 60m.

In some runners we have increased it already to 90m or 2h I think, but not all. Runner: #269 (zQGyX19F) progress.gnome.org (flatpak) seems to be 60m but there might be more runners. Could we bump it 90m or match the rest of the runners?

https://gitlab.gnome.org/GNOME/gnome-builder/-/jobs/2530556

cc @chergert

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