Been away for a few days, but I'm back and lets see if I can answer the posed questions.
So, a couple times I was asked what my efficiency is (I don't know) and if it's consistent (it is not). I have not calculated my current mash efficiency, but it sounds like I should be doing so. I haven't because, well, Beersmith tells me what my gravities should be at certain steps in the process, and I just follow that. I don't know if calculating my efficiency will be of much value because, well, it's so inconsistent. The pilsner recipe I included in the OP was came in at 1.036 pre-boil when Beersmith said I should be at 1.042. However, the previous beer I made, a British style Premium Bitter, was bang on my pre-boil gravity. Why was it different? I have no idea. Sometimes I hit my target gravities, sometimes I don't. I don't know why sometimes and not others.
In terms of adjusting my recipes for lower extraction, I generally plan about an 10% in grain to try and make my target gravities.
Ultimately it sounds like the consensus here is that I don't have enough information to know why I miss badly sometimes and not others when I think I'm doing the same thing each time (though different recipes have different mash schedules so maybe it's something in there?).
Are there common pain points that I should be on the lookout for? Is it generally OK to trust in Bru'n water for mash pH or am I a fool not to use a pH meter to check my mash? I generally feel like there's not much I can do about it once the mash is in process but maybe I should get some lactic acid for times it's too high?
Both my kegs are empty (last one ran dry last night) so I need to brew again next weekend. I'll try and religiously and see if I have better luck and will be able to provide more information to hopefully ask you folks again to get to the bottom of this.