You asked--Can you control, e.g. a good sequential list of figure captions, now that there are taken out of the text flow? I've found that they do not display in the correct order.
Why do you think that they are out of the text flow? Here are the steps to place a caption and a figure callout and sequence numbering that does work:
In your existing anchored frame, click on the anchored frame to show handles.
2. On the bottom handle drag it down so you have enough room to insert your caption and figure number callout.
3. Click on the "Display Tools Palette" to open.
4. Click on the "Place a Text Frame" this change the mouse pointer to a "+".
5. near the bottom of the anchored frame hold down the left mouse button and draw a square. Release the mouse button when done.
6. When the Create New Text Frame dialog box is displayed, just click Set.
7. Double click in the new text frame so that the mouse pointer changes back to FrameMaer cursor.
8. Enter your caption you want.
9. Assuming you have created a valid catalog item that calls out "Figure"and figure number, click on it . You now have a working callout and one that is in the flow.
10. text flow can be moved and centered or what ever you want it by selecting "Select Object" and click on dialog frame.
11. from the menu bar selecting Graphics>Align
You said--And if the caption is below the graphic, you still get the unwanted result of the hypertext marker displaying at the top most of the screen and the graphics itself hidden and outside the screen. Literally.
Sorry, if you follow the steps I outlined, clicking on the cross reference in a PDF to the figure goes to the page. I do assume you are viewing the pages as Fit page?