I don't have a Toppeak rack, but the drive side dropout does stick out more due to the torque sensor. Also the holes on the dropouts aren't aligned for perfect rack mounting so what you're seeing is normal. I use a different rack with some mods to get it centered.
The fork has these mounts & one through the arch which may be plugged. For the fork legs any strong piece of L-shaped material with two holes drilled in it.
Some tips.
Take advantage of your LBS tuneup especially with the wheels. Broke my 2nd spoke recently from spokes loosening, but this was after around 2k & 2.5k. Bought a Park tension meter so hopefully it'll be the end of that. My front wheel arrived badly dished which I fixed & has been fine since then.
Since you'll be riding in the wet, check those connectors. My CC would shut off & had sluggish assist. After a battery exchange & two controllers it ended up being a corroded connector from the display to the wire harness. I haven't done it yet, but I read dielectric grease on the connectors is good for this. Also maybe smear grease inside the steerer tube to protect from rust. Rust also developed on one of my pedal's spindle (the bushing area) making it now feel loose so taking that apart & packing some in the bushing & seal area would be good idea.
Wrap some duck tape or something protective around the chainstay where the disc is close to touching. The tightness of the rear triangle, the loose torque washers, & the spindle flats make removing & especially reattaching the rear wheel a pain & the disc will scratch/gouge the chainstay in the process.
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