Well no playbook has RnS plays in it but the Run and Shoot playbook. So Yeah Indy is a good one... if you have to sim. I mainly play in full CFM leagues so don't play the cpu a ton, but I know how that can be a grind to play all 16 games a season vs CPU... maybe just play offense for all 16 instead, or go into games you are simming and supersim them... IDK. For me the Slot WR #2 is my stud WR... I wouldnt want to sim games where his production is given to a TE... especially when I usually only have 2 cheap blocking TEs on the payroll.
Yeah the Flexbone and the RnS both have a lot of overlap, especially in the 70s and again at Georgetown University under Red Faught. What you are calling the Shootbone is something similar to that Georgetown version of the shoot probably.
As far as the option routes. They always run the correct option vs the leverage shown. i.e. if you go into practice mode and call slide vs 3-4 odd - Tampa 2. The 3 option routes will ALWAYS do the same choices every time. However, if you hot route both of the deep zones to some short zone, they won't, or if you hot route all the short zones to deep zones... or if you man up all the underneath zones... the option routes don't respond to the play call, they respond to a few other pieces of the puzzle... like what the safeties are doing, is there a middle hook zone, things like that. The Choice Route for instance vs cover 0... lets say a random 3-4 odd cover 0 play with 3 lbs blitzing and 3 lineman. if the hb stays in to block, the lb assigned to man up on him drops into a robber zone. if that robber zone is there the choice route will run a fade. If you put the HB on a pass route... a swing right or something. then that LB chases him down and there is no robber route. Now the Choice route runs the short post/slant. The option routes always run the right routes. The only hot routes I run are listed in the middle column where i list my automatic adjustments to plays... which are there moreso to make the plays in the game reflect moreso real RnS plays, not to pre-read option routes. The only routes I hot route based on coverage really is on slide vs an obvious man defense (discovered via motioning), the bubble should convert to an in route. and also vs man, I am more than likely going to put the backside wr in trips on a slant vs off man coverage or a fade vs press man coverage. Other than those 2 though... and what's listed under adjustments, I don't hot route at all.