What is better?

I think a better phrase would be ‘which do you prefer?’. AM stuff is usually a time saver. But properly made scratch built details can be superior in detail. 

I do like pre made resin seats as replacement parts, especially for older simplified seats. And some new tool kits have beautiful seats, but no harness, only a decal for the harness, so it’s a question of how to deal with that- enhance or replace? 

Politely , I disagree with the premise of the question. There is no “better”.

When asking which of something is better, it would help to know your criteria for "best."  To me the choice between modified kit parts vs aftermarket is cost. If the kit was a cheap one, and the aftermarket stuff is very expensive, I will modify kit parts. If it is an expensive kit and the aftermarket stuff is reasonably priced, I will pop for the aftermarket.  Your criteria may not include cost, however.

For simple seat belts like WW I and WW II aircraft, I like fabric belts with PE buckle hardware. It’s hard to beat the look they give when done properly.  But threading the buckles can be maddening.  In 1/72 I sometimes cheat and just crimp the belts and glue the buckles directly on.

For jets, I prefer a resin seat with the belts molded on.  Painting can be challenging, but I think PE belts look too stiff in comparison.  Plus I have had no luck keeping the colored Eduard PE belts from chipping.

If the kit comes with a nice crew figure, I tend to use it to simplify the whole seatbelt issue.

I do.  My f84 came with pe belts.  

If they include say pe harnesses do you go for it or not?

I really like the resin ejector seats.  I'm so / so with PE.  Looks great when done right, I just get frustrated with it.  Scratch building is fun and rewarding.  I mostly build box stock though.