You are right about his making season two’s filming more complex!

Before production of the second season began, series creator Rob McElhenney found out that DeVito was a fan of the show and a friend of FX president, John Landgraf. McElhenney asked Landgraf to set up a meeting. McElhenney met DeVito at his home and pitched DeVito’s character, Frank Reynolds. DeVito agreed to star in the show, but was only available for twenty days. To have Frank Reynolds in all ten episodes of the second season, all of DeVito’s scenes were filmed before filming the remainder of the season.

https://en.wikipedia.org/wiki/It's_Always_Sunny_in_Philadelphia_season_2

They ended up filming the entire season out of order to accommodate his schedule, which made for a lot of continuity challenges. They started by recording only every shot that involves DeVito. After they no longer had access to him, they went back to those same scenes and recorded everything else, making sure all the sets/costumes were the same as they were during the DeVito shoots.

https://www.youtube.com/watch?v=5QSnimzHjO8

Starts talking about this around 2:35