I think some setting must have got changed when I updated photoshop. Right now when I use the custom shape tool once I dragged it out and let go of the mouse button it remains in the mode where you can change the size/aspect ration. It didn't used to be like that, I'd have to Ctrl+t to get that. This is a change that's been really frustrating as I make word bubbles with the tool and now how to clic enter after each shape is created where as I didn't used to have to do that.
I don't know of a preference to hide the handles, but you can hit Return (Mac) or Enter (Windows) to dismiss the handles. I know it's not the same, but I couldn't find anything else to control that behavior.
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