Applying waterslide transfers over rivets/raised detail is bascially a case practice and suitable preparation and selection of suitable transfers, wetting agents & varnish/sealant.
N Scale Lehigh Valley Diesel. One my pride and joy, very much a hard worked 'layout loco' I finished the loco in LV livery about 25 years ago using Microscale waterslide decal set, incl black/white nose/pilot stripes s, Micro-Set (wetting setting agent) Micro-Sol (solvent/softner) around details/irregular surfaces. Loco painted in a gloss aerosol red then, then finished with a semi matt aerosol. Paint did not adhere too well to handrails which were molded in a black flexible plastic.
4mm Ranks Ireland wagon (Enlargement shows up the blemishes!) Decals comissioned from Railtec Transfers, Humbrol Decalfix (recommended by Railtec, Micro-Set Micro-Sol incompitaible). Main challenge was applying large RANKS (Ireland) Ltd element of decal due to its sheer size, applied RANKS (Ireland) Ltd as 3 separate decals! (Ireland) after applying the two larger decals!
Again model first spray painted grey with a gloss finish and then sealed with a matt/semi-matt finish once decals had dried out
I originally intended to have the decal pad printed comercially, but printer declined to print further wagons after pad printing the initial batch of 20T Brake Vans