A user would like to insert comments and variations and then merge multiple games to get an overall variation tree, but unfortunately, the initial moves have been played in many different orders to allow for uniformity.

 

How can you avoid unwanted variations being shown in the tree when merging games?

 

You have to return to the initial starting position (i.e. the very start of the game) and input the desired move order as a variation.  You can then go to the start of the variation, and select “Replace moves” from the “Insert” -> “Variations” menu.