one of the change included in the Sinanju OVA version is the innerframe was changed from ABS to PS. this is due to multiple complaints received when some modeller use lacquer paints on ABS (even though it is indicated in both manual and spray can that lacquer is bad against ABS)

now, most of the MG released used PS as inner frame and as you said, your proto zero already uses PS as their inner frame, feel free to use paints that uses lacquer thinners (as long as stated, that it is plastic safe)

im not a sifu but

1. seam line removal for me, at least on newer kit, is optional. Newer tech from most new model tends to hide the obvious seams. now if there is an obvious seams, then remove it first

if there is not, just go straight primer > paint

2. both methods has it merits. it actually depends on the modeller on how lazy he is or how much details he wants.
for me, i rather paint the trees directly then just do second spray on the inner frame where the nub will be clearly shown since inner frame will most likely be covered.

Now, if you want to show the inner frame details, well, you have to assemble it first then clean all the parts before painting. Another advantage for this is that you can spot the design that you have to be wary off during painting. parts that are tight without paint will be extra tighter when painted so you might want to cover it or sand it so that it will remain the same after painting

loose parts though, is good when painted since it adds additional friction.

for major filling, i used the putty found in hardstore (the one that you mix two clays together), then finish it with hobby grade putty like tamiya or MR products for easier sanding.

it is also best to let it cure for more than a day since most of them do shrink

is the cape made of textile/cloth? if yes, any paint will color it but it will harden and flake when moved. If you want, you can experiment with dye. What color you want it to be?

Anyone can recommend what Bosny gold to use for Inner frame (Momoko SF). I am planning to get 18KT gold effect from Bosny but they have different gold shade to choose from.