I am worried that once I transition from typing to taking notes that the keypad is going to pick up dirt etc since it will be face down against desk etc.
Remove the keyboard or put a paper towel or very thin cloth under it if you’re worried about that. You may prefer the feel of it without the keyboard underneath.
I ditched my keyboard cover on my 10.5 and went with a slim case. I have an old magic keyboard for when I really need it, but am finding writing on the iPad becoming second nature after a couple weeks of it.
Never worried about it and have had no issues at all - I take handwritten notes at least 1 hour each day and haven’t had an issue doing this for almost a year.