If you export a response summary from Data & Analysis, it shows the full survey, whether or not the respondent answered or even saw certain questions or blocks. I don't know of any way to customize that, or the page breaks.
The response summaries that respondents can download themselves, if enabled for a survey, are superior; they only show the questions that were displayed to the respondent. Those questions and blocks that were not displayed are excluded from the PDF. It also offers better page breaks, with help from this solution. I wish Qualtrics would make these PDFs available in the Data & Analysis exports because they are more reader-friendly than the current PDFs. I don't know how many response summaries you have to download, or if this is feasible in your design, but the only existing workaround would be to enable EOS response summaries and use those links when you need to download the PDFs.

Thank you MatthewM Matt, I tried the EOS solutions by adding the Java Script however it appears to not changed anything. Do i need to add this for every questions? Also will the changed show up on existing responses or would I need see the changes until after a new survey is submitted and I export the response to PDF.

In my experience it only has to be added to the very first item on the survey. I have not applied it to a survey that has already started data collection, so once the survey is published with the update, I'm not sure if only takes effect on new responses or will also update previous responses automatically.