A test that's good in the short term...

I have told the patrol that in order to get to an island and rescue some mice an Ob 5 boatcrafter test is necessary. Multiuse and for a whole patrol (2 mice + those being rescued).

The players may decide that they should make a boat that’s just for the two them at Ob 3. Should they then need to spend a check for the return journey. Assuming they reach the lost mice and complete the mission? Or is the Ob 3 test simply not suitable?

See “No Weasels!” on p. 87. I don’t think making a smaller boat counts as an “alternate path” here. For your scenario that would be something like using Loremouse to get some kind of critter to help out or whatever.