In the case of the Main Storyline + Missable synergy in particular we don't really think that visibility is an issue. Naturally the flags will never be used independently on the same achievement, so it can be assumed that when used together they are part of the synergy.
As we've already stated elsewhere though, for the other synergies we're fully aware that one of the main issues at the moment is their lack of visibility on site on game pages. But I assure you that this is high on our priority list; a list which as a manager for the team I prioritise.
However please understand that prior to us implementing anything we want to take to the time and ensure it's as intuitive for community as possible. There are a multitude of areas this will affect that we need to consider before hand, and I'm sure you will agree that's there no point in us rushing an implementation if it's going to cause additional confusion.
While this is a feature we would love to snap our fingers and implement within the week, that's not realistic and it's going to to take some time to get it right.
I hope this makes it a little bit more transparent, and if you have any additional questions or concerns regarding this feel free to contact me directly.