Harrison beamed 72 missiles with a single transport on a starship.
Have we seen the same movie?
Harrison/Khan had nothing to do with the transfer of the missiles.
Marcus had them transferred to the Enterprise, thus getting rid of - if the Kirk had functioned as intended - Khan, his crew and the Enterprise.
Maybe we didn't see the same movie! I thought Spock pulled a fast one at the end? I didn't see anything to indicate that Harrison left any of his people behind? Wasn't that 72 in a single transport?
The TMP Enterprise had a couple of emergency transporters that could take 20(?) people at a time but that presumably had fewer safety features. In TNG I believe they temporarily upgraded cargo transporters so transporting large numbers of people in one go is not unheard of but unusual for a single person, especially considering how proud Scotty was of beaming 3 people from two locations in the last movie - although I can see how that would be tricky for one person. Maybe they should have more than one transporter on standby?
It is a bit incongruous though isn't it? Why do you need emergency transporters at all if you can just beam 72 people to your cargo bay.
I really love the TMP Enterprise. So much thought went into making it credible and yet limited in scope (including emergency batteries, recreational facilities, and botanical labs). It evoked the pioneer spirit of our current astronauts by clearly being a cramped tin can in space but had just enough advanced features to make it inspiring.