Adam,
Rule 33-8 says:
a. Policy
The Committee may make and publish Local Rules for local abnormal conditions if they are consistent with the policy set forth in Appendix 1.
b. Waiving or Modifying a Rule
A Rule of Golf shall not be waived by a Local Rule. However, if a Committee considers that local abnormal conditions interfere with the proper playing of the game to the extent that is necessary to make a Local Rule which modifies the Rules of Golf, the Local Rule must be authorized by the USGA.
If you get a Decisions book and look under 33-8 you will see all kinds of local rules and whether they are legal or not. Also Appendix 1 of the Rule book contains a number of local rules.
The question of your limestone area is, does it meet the definition of a water hazard? If it does and it also meets the definition of a lateral water hazard, put red stakes around it. If it is lateral, put yellow stakes around it. If it isn't a water hazard do nothing and you get relief from the casual water.
As to where it transitions back to scrub, if it is well off to the side, you could either put stakes on the far side or extend the water hazard to infinity that direction. For a wide hazard on the side, where it is unlikely that someone would go even wider and it would be hard to tell, I'd extend it, but if it was narrow or the person could easily see that they were wide of it, I'd mark both sides.
For your last area, if it is something that is crossed, it probably should be marked as a regular water hazard and have yellow stakes. Red (lateral) water hazards are overused by courses. Having helped the USGA mark Pumpkin Ridge, I was surprised by the number of places they removed red stakes and put in yellow. Definitely more than the PGA Tour guys had done for the Nike Tour Championship. Read the definition of a lateral water hazard and determine if it applies. If not, it should be marked as a regular water hazard.
In your post you frequently call something a lateral hazard. I'm sure you are using that as a shorthand for a lateral water hazard, but just to be clear, first it must be a water hazard before it can become a lateral one.