Cost wise, there is no difference. As far as it goes, I'd go with the "During this period, the vehicle is unavailable for use. If for some reason the character needs the vehicle, he or the mechanic must spend an additional hour putting it back together and returning it to something like operational condition. This hour does not count toward the repair time."
While, cannonically if you do 1 box at a time, and average say 3 successes, It'll take you 4 hours to do a box, and so on.
I just noticed, the largest downside, "Replacement parts have the same Availability Codes and Street Indexes as the vehicle under repair. Characters obtain parts by using their Vehicle Build/Repair Skills to make Acquisition Tests. Repairs cannont start until the parts show up, so characters must wait out the entire Availability time period before commencing repairs."
Now, cannonly, according to that, you can roll for your 1 box, then wait whatever base time it might happen to be before you can start, and then finish your repairs, then you can wait again for the next box.
I.E. You happen to have a Toyota Elite. Base time of 8days per parts, TN 8, rolled with your B/R skill. So, say you get 3 successes on TN(3) and 1 on TN(

, well, you have 8days+4 hours to fix it, then you can move on to the next damage. TN(

repair (6 boxes) TN(8)parts, leaves you with 1 success on both (pretend) and 8days+96hours (4 days) to fix it. 12 days total, vs whatever might happen with the rest of the damage going peicemeal.