Pro Tools includes a method of animating tables by cell, row or column that has previously required complex and unsatisfactory workarounds. The table is not destroyed and can still be edited.
If you press Shift and double-click the Normal button, you will switch to Master view with the slide master selected.
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2. Yes you can use animations within the custom layouts of slide masters.
3. This may be because the layouts are no longer "following" the slide master "parent" (the topmost layout in the slide master view). To confirm, try with a default Microsoft Office template.