Transitions on connected clips

I will try.

1)

Here is the timeline with two clips (in this example, they are the Nova and Clouds generators) scaled down.

I applied the transition "Fade to Color".

At this point, if the playhead were at the center of the transition, the whole viewer would show as black - including the Curtains in the background.

2) Select Nova, the transition and Clouds and create a Compound Clip.

3) Trim the Compound Clip to the dimensions of the smaller clips. It is easier to do this in the Inspector.

In the last image, you can see that at the center of the transition, it is fully back but only inside the compound.

If you do this often, with the same dimensions, you can make a note of the numbers in the Inspector and type them directly instead of dragging the sliders.

It depends on the transitions. Some work just fine, some affect the whole frame.

The Fade to Color transition, for example, affects the whole frame.

Here is an example. I have the Curtains generator in the background, and a transition between "Nova" and "Clouds", both of which are scaled down.

If I just apply Fade to Color, the whole frame will turn black - including the background.

However, we can get this really easily:

1) Apply the transition

2) Make the two clips and the transition into a compound clip

3) Trim the compound clip to be the size of the clips

I see.

This is a third party transition, which I don't have.

I can think of two ways to handle this sort of thing in general. I can't test on the particular transition, but you certainly can:

a) add an empty clip to transition from.

You can use a clip that is transparent, or just a gap clip.

Now you can't connect a gap clip, but you can add a gap to a secondary storyline.

So turn your title into storyline, add a gap to your primary storyline (Option-W) and then just drag it to the secondary:

Then add the transition, and if necessary, use my previous instructions to constrict how it affects stuff.

b) make a modified "one-sided" transition.

If you have Motion, you can easily edit a copy of the transition and edit it to make it affect only the incoming clip ("left sided") or outgoing clip ("right sided").

Now this assumes that this is a transition created in Motion and not one using FxPlug.

I don't know if this can be applied in your case.