To fit the late 2017 and beyond pipes you must use the later mounts also.
In the later part of the 2017 production run the rear exhaust pipe was tucked in a bit tighter in order to lessen the chance of leg burn or rain gear melting. It nessitated a change to the muffler mounting.
Indian doesn't make the stage 1 black mufflers for pre 18 because like you said they changed the rear head pipe.
I bought a set of later model black stage 1 mufflers off CL for $250 (yes the OEM $800 ones) after measuring the distance between the mounting tabs and comparing the measurements to my 2016 Scout 60 mounting tabs and the distance between the holes in the mounting bracket. They are the same. On the later models all 3 bolts go in from the backside.On the 2016 the front bolt goes in from the front side because you bolt the bottom muffler on first to the bracket then the top one. On the later models you have to slide both mufflers on to the head pipes then install the 3 bolts from the back.
Because of the change in the rear head pipe you have to purchase a 30mm long 8mm x 1.25 pitch bolt and I used a 5/16 lock washer and 3 5/16 x1 1/4" body washers. This is the new bolt you need to put in from the back side of the front hole in the mounting bracket. You can reuse your other 2 bolts for the other 2 muffler tabs.
To get the front muffler tab to line up with the front hole in the bracket you have to slot the hole downward about 3/8" of a inch. This is because of that change to the rear headpipe in 2018. The other holes line up fine.
Cover the caliper with a rag and use a 5/16" drill bit with downward pressure. The bracket is cast aluminum so it is easy to slot. Don't use a whole lot of pressure and turn the bit at a medium speed and be patient. Then vacuum up the debris. Slide the bottom muffler on then put the bolt in from the back leaving some sticking out, then slide on the top muffler and start the bolt. You may have to pull upward on the top muffler to line up the holes.Once you get the front bolt started the others are easy. Snug up the bolts making sure the gap between the mufflers is even front to rear, the snug them up real good, tighten the muffler clamps then tighten the 3 bolts the rest of the way.
So yes the late model mufflers will fit. You have to slot the front hole in the bracket and purchase a bolt and washers for 2$.
I used a decibel meter 8ft behind the bike pointed straight at the exhaust to mesure the difference between stock and stage 1.
idle stock 73db stage 1 76db
3600 rpm stock 82db stage 1 85db
Revved hard stock 95db stage 1 98db
Stage 1 mufflers are plenty loud and wont make your ears ring. For comparison same test with crusher mavericks
3600 rpm. 105 db
revved hard. 120db
The stage 1 are plenty loud and wont make your ears ring. Thats why I wanted to make them fit my 2016
They sound good too. If you dont change your air cleaner no need to recalibrate the EFI