[jonnyl]

Not directly, but as a workaround you could enable Custom hidden flows (Top menu - First tab - Settings - X Custom hidden flows). Then open Page browser, long press on the first page's thumbnail and tap 'Start hidden flow here'. Then on the page you're reading from, long press, and select 'Restart regular flow here'.

You can also add a second hidden flow area if there's any back matter (index, notes, etc.) you'd like to exclude.

The calculation will now be based only on the pages contained in the regular flow.

Edit: Actually, the calculation should already be based on your current position in the book anyway, regardless of whether the previous pages are marked as read or hidden flow. The remaining time for the book may seem incorrect because after only some pages read the average time calculated per page may not be accurate yet. However, the average calculation should only be based on the actually read pages. (With or without hidden flows.)