Since the comics came out in between The Search for Spock
and the next movie, Paramount didn't want the comics to make any major changes in the status quo that existed at the end of TSFS. And the status quo at the end of TSFS was that Spock was alive again but wasn't necessarily back with the crew. They didn't know what the fourth movie might establish, but it stood to reason that if it showed Spock rejoining Kirk's crew, it would probably play it as the first time that had happened since his resurrection. Or maybe it would show Spock having his first major conversation with Kirk or McCoy or whoever since he was brought back. They couldn't know what might happen in the next film. So it was just considered safer to keep Spock sidelined.
storyline was also a response to the need to maintain the end-of-film status quo -- they couldn't give Kirk a permanent new command before the fourth movie did, so they had to set up a temporary situation with the Excelsior
that would let them keep telling starship-adventure stories until they found out what would happen in the fourth film.
Also, it was during Len Wein's run (which overlapped TVH) that Spock rejoined the crew of the Enterprise
-A, a status quo that lasted through Mike Carlin's run and finally Peter David's. David only wrote eight issues at the end of Volume 1 (and then came back for Volume 2).