Oho, yes -- MCell-style floating selections! I recognize a lot of the icons from the applet, too... It took me years to move to Golly from MCell, and it was mostly because I didn't want to leave behind those amazingly handy floating selections. (Since then I have managed to get used to Golly's background-type selections pretty well -- among other things, it turns out that they're pretty useful for marking reference rectangles to paste patterns into, often from one layer to another.
In MCell, I especially liked being able to select an object to "float" it, then grab it with the mouse and move it wherever I wanted, run the rest of the pattern as long as I wanted (sometimes allowing gliders to pass right under the selection!) -- then click outside the selection rectangle to drop the floating selection back into the universe again.
SquareCell doesn't seem to work
quite the same way -- it would take me a while to get used to that Ctrl key functionality. Also, does the SquareCell executable work slightly differently from the applet? In the applet, when you grab a selection to drag it around, you always suddenly end up holding it by the upper left corner, which is a bit annoying if you want to line up some other corner with something.
The executable does things a bit differently, no sudden jumps to the upper left corner, but you still don't end up with the mouse pointer fixed on one point of the selection -- and for some reason you get a floating copy of the pattern, but unlike in the applet, the original pattern is still underneath and has to be cleaned up somehow. Is there some way to change this behavior? I couldn't see where a setting like this would be.
Anyway, yes, this kind of thing can "make phase adjustments... as you're moving pieces around". But it's not quite what I meant by "on the fly"! The idea there was that because of a glider stream or some other periodic connection between components, different locations for (let's say) a reflector might automatically imply different reflector phases.
So I still don't know of any programs that automatically adjust the phase of a reflector as you're moving the reflector around, so that the reflector will still automatically work in its new location without any manual rephasing. Rephasing, so far, is always a separate operation -- and it does seem awfully hard to make it an automatic consequence of moving an object, at least in a general-purpose way that would be really usable.
Another wish-list item just occurred to me (not for SquareCell, just for my hypothetical super-user-friendly Life editor): If you click and drag one reflector in a chain, and a nearby reflector is feeding it gliders, and/or another reflector is catching the gliders that it reflects, it might make sense to automatically move those connected reflectors so that they still line up with the one you moved, and rephase the whole chain appropriately so that it still works.