Actually, Space Quest VI wasn't designed by Scott Murphy, at least, not entirely. Scott was done with the series after the fourth game, between his falling out with Mark when Mark left Sierra for Dynamix without telling Scott anything about it until the day he was moving, and Sierra constantly pushing their business decisions over Scott's design decisions and meddling with the game production. That whole scene in the third game, with Ken Williams whipping the programers at ScumSoft, that was Mark and Scott's way of giving the management the middle finger. And if it was up to Scott, Space Quest IV would have used the text parser of the older games instead of the point and click interface, Ken "gave him the choice" to either use the text parser engine or the point and click engine, Scott chose the former, only to discover the next day that, even before they "gave him the choice" the big heads above had already decided to go for the point and click engine and if they asked for his input it's because they figured they had a 50% chance he would have agreed with them.
So, Sierra wanted a fifth Space Quest game, they asked Scott but he wasn't interested, Mark was gone and he was done. They asked Mark at Dynamix and he agreed, and so Space Quest V was mostly Mark's. Months after the release of the fifth game, Josh Mandel pitched a couple of game projects to Sierra, one of them was a sequel to Space Quest V. Sierra green lit that one and Josh began designing the game, but halfway into the development, Josh had a disagreement with Sierra and had to leave the company. Sierra found themselves with an half finished game in need of a lead designer and so they decided to parachute Scott in to finish it for them. That's the reason why, although the game has all the right ingredients to be a great Space Quest game, with Gary Owens' timeless narration, the great graphics and animation, a fantastic soundtrack and a game length that outclass its predecessors, some sections nonetheless seems halfway done or rushed, like the Datacorder puzzle, the obtuse puzzles and lack of in game clues in the last part of the game, and the whole "Where the heck is Bea? And who is this Stellar anyway?"
Late into the production of the game, Scott called Josh regarding fake comics and magazines he found in the design documents and he had no idea what those were for, Josh told him those were supposed to be found in the apartment of the goons that kidnapped Roger, and you were supposed to read those to get your clues on how to turn the Datacorder into a beacon. Unfortunately, that info came too late into the development process and Scott had to put that info in the manual at the last minute, transforming that puzzle into a copy protection kind of puzzle.
Josh had plans for all of these other WTF moments in the game, Stellar's relationship with Roger was supposed to be explained in more details, there were cutscenes with Bea that were planned, the Inner Space chapter of the game would have received more in games clues both from funny messages as you examine the rooms inside Stellar's body and from various documentation, not unlike the fake comics and magazines from the original Datacorder puzzle... but he had to leave the company and whatever ideas he hadn't written down or explained when he left the company left with him.
And if you want to witness just what the game lost when Josh left, go in the Elevator room in Dr Beleauxs' laboratory, the Elevator room and the screen with the buttons to go to different floors, in these two screens Josh wrote a unique and hilarious line for every possible combination of Eye/Hand/Mouth icons and hotspots in those two rooms, cleverly turning what has to be the most boring location in the whole game into the funniest location (do a Youtube search for the funniest lines in Space Quest VI and you'll see that a quarter of all the lines in those videos comes from that room alone). That, right there, is Josh Mandel's unique touch as I like to call it, he loves doing that, I read that he did the same thing with a few other games, noticeably he did that in the recent remake of Leisure Suit Larry, going out of his way to make sure no matter what you'd click on, the game would reward you with a funny and unique message.
And we can't really blame Scott either, he got parachuted in at the last minute to cover for Sierra's mistakes, his vision of Space Quest was entirely comprised in the first to the fourth game and here he was, finishing somebody else's sequel two games after he left the series, and it's not like he could have mind melted with Josh to magically learn everything Josh had planned for the game. Really the only people we can blame for the shortcomings of this game is the management at Sierra for departing with Josh, because that game would have been so different, much better IMO, had he carried it all the way to the finish line. Sierra even went as far as to remove his name from the credits and, for marketing reasons, pretend the game had been solely designed by Scott.
As for the memorabilia in Roger's room, those were by no mean an attempt by Scott to ignore the existence of the fifth game because the Space Quest VI Interactive Demo was developed back when Josh was still involved in the project and the demo featured a short original episode set in the Deep Ship 86, and that included being able to go in Roger's room to pick up items and look around at the memorabilia. And considering the early games had Roger toiling for nondescript space organizations and that every game had a different vibe (the remake of the first game had that Flash Gordon and Buck Rogers, fifties pulp sci-fi feels to it, the fourth game lampooned Terminator and time travel in general, and the fifth game was a huge homage and parody to Star Trek,) even if trinkets and memorabilia from Space Quest V are missing from Josh's design, the fact that Josh kept Starcon around and continued the Star Trek parody during the first two third of the game plus a demo, that would ultimately be the legacy the fifth game had on its sequel. Roger's memento from Space Quest V is the huge Starcon triangle he's now wearing on his uniform.