I see what you're getting at but I don't believe that it's a significant problem in weightlifters with well organised training for a few reasons:

The high bar squat also trains the gluteals very effectively, due to the large degree of anterior knee travel reducing the hamstring contribution to hip extension. Furthermore the greatest part of knee extension forces are generated by the vasti, which do not contribute to APT. If you have an athlete who tends to shift the knees posterio-medially rapidly in the squat ascent it can be a sign that they have insufficient glute strength and are loading the hamstrings to compensate. Cue glute strengthening/activation and a focus on standing straight up in the squat, with simultaneous knee and hip extension.

Personally I see back extensions as an exercise to develop thoracic extension strength and postural control primarily. For this purpose they should be performed with a braced neutral or slightly extended lumbar spine, so they should not lead to APT. The alternative method of flexing and extending the lumbar still has obvious benefits in terms of lumbar extensor hypertrophy though. For either purpose a well designed program will include similar volume and intensity of abdominal training to balance against the spinal extension strength.

With regards to back extensions and disc injury: Dr Stuart McGill has written extensively about lumbar flexion/extension exercises increasing the chance of lumbar disc pathology. Also it's worth keeping in mind that stable lumbar extension is better than unstable neutral positioning, as the main concern for injury is loaded flexion or extension irrespective of starting position. Hence slight extension may be the safest option in addition to optimising force transfer.

Finally, weightlifters should have excellent flexibility, so shortened hip flexors should always be addressed with appropriate stretching.