Option #1: no, it should work just fine, because all stations in a program are affected by the same watering percentage. Say if the watering percentage is 50%, then all station water time is reduced to 50%, hence it’s still correct.
The only downside of Option #1 is that the master station is managed manually and is associated at per-program level. Say you use station 1 as master. If you manually turn on station 2, it won’t automatically activate station 1 as it’s not configured as a master station.