Yes, although this matter is largely one of preference and habits long-formed.
I agree with Parker, and will make one suggestion. In each batch do one or two bottles in the threaded bottles. This way you can see how it works for you while endangering only a small fraction of your beer babies.
If you don't have a bench capper, then you'll find that it is better to use non twist off bottles. Some people who have tried with their standard wing capper have broken the bottles.