It sounds like you are trying to get Adjustment Layers
to do something that they were not designed for.
You have obviously found the best workaround,
but you might want to file a Feature Request anyway.
In addition to that I adjustment layers would have been useful in that case so that you can onitor your scenes using one track. Fo instance I have also tried to apply the same transition on the adjustment layer track with different effects and the video track but they transition differently, I think this needs a fix. For instance you dissolve from a day to a night scene...
There does seem to be a bug when using transitions between adjustment layers. I solve it by adding a 'blank' Crop effect to the layers.
Maybe, i don't know: it seems like a straightforward bug or oversight to me. You'd have thought they might have expected people to want to use adjustment layers in this way. It's quite common if, for example you have two clips with some kind of transition to want to be able to match the transition in the adjustment layers on top of the clips.
Something else - off topic - that seems a bit clunky is that you have to "create" an adjustment layer, which then appears in the project pane, then drag it into the timeline, then add the effects, etc.
But those effects aren't then associated with the adjustment layer in the project pane; it is still empty and you can drag it on top of another clip and start adding effects again. This works fine, of course, but:
(a) It's a confusing metaphor, as they say
(b) It would be handy to be able to keep adjustment layers, complete with effects, to use again (I know you can copy and paste them in the timeline, or alt-drag, but still...)
Well I am not sure whether this could be just the adjustment layers only or the transitions as well. If I apply a colour effect on my lower thirds and apply a transition on the lower third it appears the colour effect will not be applied until the transition is complete, same applies when I transition out. So this means that the viewers will see two colours of the lower third.
You'd have thought they might have expected people to want to use adjustment layers in this way. It's quite common if, for example you have two clips with some kind of transition to want to be able to match the transition in the adjustment layers on top of the clips.
It would be handy to be able to keep adjustment layers, complete with effects, to use again
I disagree on this one. I use the AL throughout a sequence, and each instance doesn't always get the same effects. Copying the layer is much more efficient than having a dozen different layers in the bin.