Casper, I agree. We should all be flying iaw the AIP and if the charts are wrong then they should be changed but it looks like the only error in our charts is that it doesn't say "or as directed by ATC" and this doesn't appear to be causing any problems. The track violations are probably pilot error. It may be that a specific fleet or airline has a convention whereby they incorrectly delete TONIC or STELA but I've never seen it, and if I checked an approach entered that didn't have it in then I'd ask the other pilot to change it.
As to treating the heights at TD and LIMES differently, for 07 I want to be slightly above 4500' at LIMES and if I leave it in the FMC then I can be. It also has the added benefit that if I'm cleared high speed below 10000' and it's busy, the associated speed restriction gives me a safety net on 250kts below MSA in the unlikely event that I've deleted the 240/1000' restriction, am in VNAV and have forgotten to slow down. I'll quite often delete it as I get a bit closer, but I don't feel compelled to do so simply because I've been cleared to a lower altitude from way out. For 25, I want to be slightly below 8000' at TD so I have to delete the restriction in the FMC otherwise it'll capture 8000' and I'll be slightly higher than I want to be.
I don't know if we have the possibility to take Air Traffic Controllers on a jumpseat but if not then it must be possible to take you in a flight sim to demonstrate - anyone know if we can do this?