You can set each page transition manually in Acrobat Pro after the PDF has been created.
- Open the PDF and expand the Page Thumbnails panel on the left sidebar.
- Make sure you are viewing at "fit page" scale so that clicking a thumbnail highlights it completely, or the next step won't be available.
- Select the page(s) you want to have a specific transition time, and choose "Page Transitions" from the panel's options menu on the top left corner.
- Under "Page Range" select "Pages selected in Pages panel".
- Set "Auto Flip" to the required time (you can type in the box if the value isn't one of the standard list).
- Click OK, and repeat for all the other timing configurations your document needs.
- If you want specific pages to not advance, just set their transition so "Auto Flip" is unticked.
Transitions will only run when the PDF is in Full Screen mode.
Sadly I don't have Acrobat Pro at the moment (and I already used up the trial version). Seems a trivial thing to have in InDesign. I'm surprised it lacks such an option.