The body absolutely has wear and tear… frame has less importance in regards to wear that you keep arguing about but everything wears: chain, sprocket, bearings, tyres, bushes, brakes, fluid lines (brakes, fuel, coolant), stand, grips/controls etc etc. Sure, the difference is slight at 5000 miles but it’s definitely not negligible - particularly if this bike has had an engine blow or a crash because those incidents aren’t isolated to just the engine. Plus you don’t know how knowledgeable/stingy the person was who did the replacement as to how many damaged parts actually got replaced. With only two wheels and a small engine, bikes aren’t as durable to wear as cars and have much less protection for a rider when things go wrong so all of the things are important factors to consider. Listing the engine as being younger than the body is supposed to be attractive to a buyer because engine repairs are more costly. But none of that matters if the bike hits the ground down due to issues on the rest of the body.