In-Game Time has been added to the leaderboards. In-Game Time is the sum of the times obtained in the levels (using the in-game timer) and bosses (using RTA to the decimal). For Any% w/ Cheats, only The Hindenbird is included. You don't have to include In-Game Time when you submit a run - a mod will do that for you. Runs will still be ranked by Real Time, as they have always been.
This inclusion allows for an easy way for everyone from runners to people who've never seen the game to compare the actual quality of runs, since loading times in this game are, to put it shortly, disgusting. You can save around 10 minutes just from switching from GCN to PC, for example.
The reasons In-Game Time was chosen as opposed to Time Without Loads are:
1 - In-Game Time is much easier to calculate (plus, I already keep track of it here: https://docs.google.com/spreadsheets/d/11V38_Jn2-YQlNAFtAvGUoJ_Rsg3e-u0mbZzv-JDcYM8 ) 2 - It's not easy to determine what a loading screen is anyway: those blue screens clearly are, but there are also time differences on the dark screens after pressing Start to start a boss fight and before the hint videos start playing on the main levels. Even the time it takes to start the game after creating a new file is both random and different between versions.