If TG was serious about legit scores, they would pretty much throw out every and all high scores from the 80's and 90's and most of them from the 21st century. The rules have changed over the years making the scores bogus.
+1. And the fact they didn't keep track of settings or ROM versions back then.
Ok, as for Free Play settings...
Having written a few free play hacks myself, the code does, logically, have to take different paths when dealing with free play. I mean, the code basically looks something like this:
//entering code that checks if a person is dropping in a quarter during game play
Check input for dip settings
If dips set to free play, jump to END
check input for credit
Credit not triggered, jump to end
.
.
<code for coin actually dropped in>
.
.
END
So, in practice, maybe the non-free-play sequence executes like two more lines of assembly.
For all practical purposes, I don't see this making a difference, but TG is trying to make the apples to apples comparision as close as possible.