Cross Dissolving, Fading In/Out and many other effects can easily be achieved in OpenToonz.
A question was recently asked regarding Fade In/Out effects and the following is a walkthrough of setting up a Scene/Level for that:
Firstli, we can simply Right Click on our Column/Level in the Xsheet and select 'Add FX' but... that may not pipe the results of that FX into the output we desire.
Generally it is better to open the Schemetic view (via selecting Windows>Schematic on our top menu) and the add the FX there.
In the Schematic view we can easily see the flow of FX and make adjustments as necessary.
With the schematic view open
Right Click on the Column/Level node we wish to have fade in/out
Select 'Insert FX>Layer Blending>Transparency
Now we can edit the values of that transparency on any frame.
There are several ways to do this.
The first would be to move to move to our desired frame and then Double Click the Transparency node to display the node's properties.
Change the property (or type in 0) to set a keyframe of no transparency.
Move to the frame where we want to have the image fully transparent and then type in the value of 100.
Now our image will change from fully opaque (not transparent) to transparent over that range of frames.
Here is another topic that outlines the basic process: