Sigh.
I don't know if there is an easy way, but I can tell you how I did it.
Step 0:
Make a new project.
Step 1:
I made a backup of my RTP to another folder.
Step2:
I deleted anything I didn't wanted for my project from the RTP
That made a very small RTP containing some SFX and Music and some graphics.
You can even empty all the RTP and keep it empty then include all assets as extra files.
Step3:
You have to get in the new project's database and erase anything that is using missing files.
You should consider checking the database for invalid asset calls. For instance if the database is searching for a music fx for the cursor, that you deleted, you will have a problem.
System, Tilesets, Animation, Enemies : Check these if you deleted sound and graphics.
Armor,Weapons,Items,Skills,Actors : Check these if you deleted the iconset.
Step 4:
After making sure everything is ok and the game runs well, save the project as a starting template for your spripped rtp.
You need a brand new project because events can call music, sfx and graphics. Events also might have set own graphics.
It is very hard and time consuming to fix all these not to refer to any asset stripped from rtp.
Step 5:
Make sure you know where the original RTP is, so you can include it back if you want to.
Step 6:
Make the game.
Step 7:
On creating the game, you will tick include RTP. That will make the lightweight stand alone executable game.
Hope this helped you.