The Freeze checkbox (Palette)

can this be used to make a meaningful transition between scales? 

 Of course yes. As janamdo already wrote, you should use a common -or pivot- chord. It's quite easy if you highlight the scales you wish to use to modulate to/from

You could write a very simple progression for a piano solo using just two scales, for example, and just one looped figure.

Synfire will take care of the rest, computing a not-so-bad, eight measures phrase. Not a masterpiece, indeed, and I would then export it in Logic or StudioOne to tweak it, change several notes, instruments, humanize and so on: this is a prototyping software, not a DAW ;-)

In the attched file I picked chords from two scales: a Natural Minor #6 (that is: Blues-3) and a simple C-rooted-Major. You could consider the Cm chord in bar 5 as a pivot chord, or, better, a modal change chord from C Major Scale to Natural Minor #6, but actually I picked chords from either scales across the 8 measures.

If you select the Major scale in the Palette, you may instantly see how many chords (in blue) your two scales share (the shared chords will be those above the natural-minor #6 line), and test several progressions on the fly. Usually I click back and forth across two or three chords to get an idea of the mood. Then, when I find a satisfying sequence of chords, I drag them in the upper progression track and test them with my looped figure or with a sketch preset from Playback menu.

If you forget which chords you played, you can track back them using the left-arrow key on the computer keyboard.

For a reason I don't understand there is no way to do the opposite (move forward) using the right-arrow key.

The "History" window is either unclear, to me.

In this 8-bars phrase I picked four chords from the upper side of the palette, the natural-minor #6 scale: Dm7-D#(add9)-F-Gm7(#5)

in measures 5-8 I simply did a copypaste of the above chords and raised them one semitone up.

I then substituted the default Yamaha piano with a more comedy-like duet of Electric piano and Clavinet.

Note that the whole phrase uses just a two-bars Figure for the EP part, and a 1-measure accompaniment in the Clavinet. 

Synfire did the "arrangement" on my chord progression ;-)

Dm7-D#(add9)-F-Gm7(#5)

The second chord should be read Eb(add9). There is a way to change chord names, but for now it's not a life-or-death matter ;-)