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Would it be possible to move the 'TIME BONUS' part of the hud so that it does not take so much vertical space?

Yes, it would be possible. I actually chose that position so that it would be possible to add a second player (for split-screen co-op), but just didn't end up doing that.

I don't think it's worth it to make a new release for this change (especially since there's still a chance I might add 2-player in the future, though unlikely, and I don't see the additional use of vertical space as harmful), but if you would like the change, you can replace these lines in retux.py (around line 530):

text = "{}\n{}\n\n{}\n{}".format(
_("Score"), score_text,
_("Time Bonus") if time_bonus >= 0 else _("Time Penalty"),
abs(time_bonus))
sge.game.project_text(font, text, sge.game.width / 2, 0,
color=sge.gfx.Color("white"),
halign="center")

with these new lines:

text = "{}\n{}".format(_("Score"), score_text)
sge.game.project_text(font, text, sge.game.width / 2, 0, color=sge.gfx.Color("white"), halign="center")
text = "{}\n{}".format(_("Time Bonus") if time_bonus >= 0 else _("Time Penalty"), abs(time_bonus))
sge.game.project_text(font, text, sge.game.width, 0, color=sge.gfx.Color("white"), halign="right")