On the side of boxing vs. not boxing, my feelings do change quite a bit about pedals, and if I box things, I'm more likely to play the pedal and discover its interesting parts and good settings. This is especially true of pedals that don't shine by themselves, but work best paired with something else, like say, the Lycan Overdrive, or the Moonn 200 Sunny Sunns.
OP, just to be clear/er, I solder in everything before drilling, and I just making sure the bodies of pots and switches are flush and level with each other so there aren't differences and gaps between them and the enclosure. I broke two mini rotaries in the heterodyne receiver installing into the enclosure, and I'm pretty sure it was gaps/differentials between the switches and the pots that cracked the switch body apart.
If you pay attention to that, you should be good, then you can proceed to testing, and drilling the enclosure for the circuits you want via careful measuring, a good ruler, a step bit, and a hand drill. It's really the only thing I can think of to pay close attention to in preparation for possible boxing. I usually install the jacks and 3pdt as well, but you could do the auditorium route to save money on those as well. Disadvantage is that a lot of playing unboxed circuits with jacks and switches means usually one of the jack leads will break and need to be resoldered.
For the record, I also only install LEDs after drilling and boxing, if that.