Yes, Matt has outright said that sometimes things in their Journals are trials to see if a particular idea is popular and worth including in the future core.Note that just because something is in JTAS that doesn't make it canon, there have been many article both in the original GDW JTAS, the GT JTAS, and now the MgT JTAS that are fanon and IMTU things rather than official add ons to the core books.
Now for pop up turrets, I would make it so a pop up mechanism has the same displacement as the turret or barbette that is going to "pop up".
As to batteries powering weapons, yup perfectly allowable and a good way to hide your combat potential.