Unless something is designed to be used with the WOD, as written (like Rutherford's ME Black Box), it's not an easy drop in.
Let's say the WOD is:
Would you want to warm up with intense work on split-squats, step-ups, bulgarian split-squats (leg elevated), or pistols?
I'd say "No." Your main focus would be to reach a high level of performance on the 5x5 squats.
You could very successfully follow up the 5x5 squats with unilateral work, though.
You have to go back to the original question: What are you trying to do?
If your answer is "to be as ready as possible for anything that come up" then your course of action is going to be significantly different than if your answer is "I want to total 1800 lbs in equipped powerlifting competition" or "I want to make the regional select-side for rugby".
Despite all the suggestions to the contrary, specialization is a requirement for high level compeititon or performance. If your goals are specialized, then your training towards that goal is going to be specialized.
If that goal is a sub-120 second Fran, then you are still going to be specializing in improving certain aspects of your performance to reach it...namely pull up ability, and maximal strength on the thruster (which is going to lead to better and faster gains in the strength-endurance or power-endurance capabilities)