Let's start with the easy one: leaving out R9 and stuffing R3 only is fine: this sets the switch frequency, and the default frequency with 52K should be fine.
So R5/R6/R8: the design is meant to be either adjustable or fixed. If you want a fixed output voltage, you omit R8, and stuff R5 and R6. You then bridge across R8.
However if you want adjustable output, you stuff R8, and you short across R5 and R6: a short piece of solder wick does this job well, or you can buy SMD 0 ohm resistors if you want it to look clean.
If the BOM says "omit" R5 and R6, that is my fault, it should read "short out R5 and R6".