Why no soft mutation on the verb?
There is no need to mutate after pryd?, pam?, ble/lle?, sut? (when it means 'how?')
So it's the same as the difference between using ydy and mae in questions?
Yes - those four should always take mae rather than ydy.
How does the usage differ among: pam, pryd, am faint o'r gloch? Also, why is it ar amser but mewn pryd? The prepositions already contain the on/in distinction, but why different nouns?
So leaving the chi off is too literary then?
For this introductory course, yes.
This course does not cover the formal registers, nor any but a very few dialect variations, nor very informal Welsh.
Why no informal (ti) option?
pryd cyrhaeddi di just worked ok.