Longer post than I originally intended but there's actually a lot here available. The tldr is the last paragraph. If it makes sense, great. If not - read the rest.
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First note, at any time, you can "experiment" to see how your current settings would prioritize the current configuration.
Click that button - it'll run through and say: "This is the order I
would have used if it was a real run."
Can tweak your settings and try again.
NOTE: In testing this, seems a bug with this preview has crept in. You need to restart the script after each run or it doesn't reset properly. I will correct.

There is quite a bit of control that you have over how things are prioritized.
The first level is what order to prioritize the priorities. Default is
Levels > Duration > Rarities > Types.
This means it should first look at level (
5 > 4 > 3 > 2 > 1). If you have only a single level 5 in the available quest list, it will be selected first (assuming it meets other criteria)
Sounds like you want Rarities to come before Duration. That means changing the priority of priorities :P
On the basic config screen, you can select WHICH of each type is run. "Should I run 24h quests or not". But the PRIORITY order of those can be seen in orange at the top of each section.
Here is it set to only run 12 and 6 hours. And it'll prefer 6h to 12, all else being equal.
You can change this order by going into Advanced settings. This lets you manually type (no pretty interface here, sorry) the order you want. For me to flip those above, click [Advanced], type what you want in full, and click the [Durations] button.
So! After this long explanation, it sounds like what you want is to change that priority of priorities - so do that.

This should mean that a level 5 Elite will run before a level 5 Common - regardless of Duration or Type.