Pauliau, Ctrl+Alt as AltGr is a pitiful Windows-specific workaround, not a solution.
I'm a programmer too by the way, but unlike you, I use AltGr all the time, because I hardly ever switch keyboard layouts, keeping Lithuanian as default (did you know you can enter all the numbers and other top-row symbols without switching from it?). On the other hand, I don't use PageUp/PageDown very often, and I don't think I could care less about the right Ctrl. These are usage patterns however, and they're personal: mine might be different than yours. Somewhere in this thread there was another programmer who said that requiring Fn for PgUp/PgDown is a no-go.
By the way, I think I would find it rather uncomfortable to press Right Fn + Arrow keys for a commonly used function: I just tried to emulate that by keeping my thumb on my Right Ctrl key and pressing arrows: in all cases it feels stressful to the wrist, or really awkward at minimum. Are you sure it's just the lack of muscular memory that makes it problematic?