Thank you for the additional explanation and screenshots. This greatly helps with understanding your workflow.
The Print-dialogue Scaling option is clearly not intended (or able) to remedy the problem that you now clearly illustrate.
Despite considerable effort to do so, as yet, I remain unable to replicate the specific scaling issue that you illustrate. I have taken sample notes from my own iPad - and systematically tried every combination of markup, markdown and associated methods of creating a PDF export that I can conceive...
While export markup/markdown does, seemingly intentionally, reduce the page scaling and introduce whitespace to the right of the text (presumably to accommodate additional drawn or handwritten material), I have not reproduced the very significant scaling reduction that you clearly illustrate in your screenshot.
For reference, for the purpose of this exercise, I am using an iPad Pro 12.9" M1 with iPadOS 27.0.1 installed.
Whilst I will continue to explore this issue as time permits, in the meantime I strongly recommend that you seek technical assistance directly from Apple Support. Be aware that if the Level #1 assistance/triage that you will initially receive doesn't provide a ready solution to the issue, you may need to constructively request escalation to a specialist that can better investigate and explore the problem with you. This escalation, if needed, may take some polite persistence on your part.
You can contact the Support Team using the Support link at top-right or bottom-left of this page. Alternatively you can initiate and manage your support cases from Apple devices using the excellent Apple Support App. If not already installed, the App can be downloaded from the App Store:
https://apps.apple.com/app/apple-support/id1130498044
Whatever the outcome, please return here with any new information that you encounter - either from Apple Support or through your own experimentation - as this will no doubt help others that encounter a similar issue. I will also endeavour to return here if I should uncover something that may help - or to respond to any updates that you may be able to add.