SCID not recognising transpositions I like going through open variations and taking notes and saving them in my database.

However I have a problem. When I get to two of the exact same board positions and same color to play, if I got there via two different variations, any future variations I make and comment will be considered separate.

For example, suppose I start a game with 1.e4 e5 2.Nc3 Nf6 and add some variations with, e.g., 3.Nf3 and 3.Bc4 and make some comments.  Then, in the same database, I add a game with 1.Nc3 e5 2.e4 Nf6. This leads to exactly the same position but the variations and comments from the 1.e4 variation are not shown.

How do I merge these variations or get SCID to understand that it's the same so it shows the variations after both move orders?  I don't want to write a whole new tree and branches just because I switched up one move.

Or if anyone knows a different program I can use for this to save uncompleted games such as opening variations and I can write my notes that would be great.
When you add comments, they exist on the current game only. If you want to comment on the position (independent of any individual game), you can do that by adding a mask.

The tree window shows you statistics on the current position (moves played, etc). Masks allow you to add additional information on top of that. Here is a resource to help get you started:

https://sourceforge.net/p/scid/wiki/HowToUseMasks/