Jaydee hi welcome to the forum..
I don't mess with the transient markers on full tracks, only on loops to get them quickly quantized. With most digital songs though it should just take two markers, one in front and one at back to get it perfectly tight.
I don't even bother doing the 'set here' function as I just manually slide the first beat to where it needs to be. But overall sounds like you're doing it properly.
The transient markers might look off if there is for instance swing or 'groove' stuff applied so I would only worry about getting the kick on at the start and end like you have.
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