It is worth pointing out that incorporating fully annotated lines is simply not possible. Many of the 50,000+ problems available in tactics trainer were pulled automatically from previously existing games, not created from scratch. Also, going back through the problems that already exist to add annotations to the sidelines is not a worthwhile time investment.
You've already mentioned a potential solution is to simply open up another chess program to work through the alternate lines. The ability to quickly translate chess notation into coherent variations is itself a useful skill to have, so it's not like you're wasting your time by having to work with your own analysis board.
I think an upgrade to the software for tactics trainer would make it much easier and useful for beginners like me. Sometimes I don't see why a particular tactic is correct. And others will comment that they don't understand either. Then somebody says, you obviously didn't look at the source and analysis. Well, to beginners, sometimes that just isn't helpful. Looks like a bunch of random text lots of times.
It would be nice instead of providing text, actually converting that text into playable lines, so that you can actually see the moves on the board, as well as annotations for those moves for the different lines.
Many times I will make a move that seems correct to me but the analysis text just doesn't clear it up for me. I have to get out another program and type in the current position, play my desired move, and then see what the computer says. If I can see the moves being played, I have a better understanding of why my choice was incorrect. Plain text doesn't do it for me.
I guess what I'm saying is the current analysis and source requires another program or an external chessboard to work through it. For beginners especially, integrating this into playable lines would make it much easier to see and learn from our mistakes. Fully annotated alternate lines would be the best.