yes, you can have no sub & run MCACC. It will detect that you have no sub and set your speakers to Large. in this case, Large means the front speakers gets the full spectrum.
keep in mind that Pioneer implements a global, universal crossover, and cannot be independently adjusted for individual speakers, so one size has to fit all. in this case, since your rears & center probably can't go as low as your fronts, you would set them to the lowest -3 dB freq they are rated for or use the THX standard: 80 Hz. if they are small satellites, you'll probably have a crossover of 100-120. but if they are bookshelf types and capable of 60-80 Hz, then use the THX standard - 80 Hz. unless your rears & center are also capable of the same bass response as your fronts (40 Hz), you would NOT set the global crossover to a number lower than 80 Hz because then you'd lose freq's the rears & center can't reproduce.
when you add a sub, re-run MCACC, & it will detect it. 40 Hz may be acceptable for music but does not include the full LFE track. you could leave the fronts as Large in which case the sub & the fronts will get re-directed bass from center & rears. while you could leave the fronts set to Large, you would be better off setting them to Small & let a good sub handle all the bass chores for all channels.