If you’re squatting for overall benefits and not for some type of competition, I don’t see why there is a need to lock the knees at the top. Your knees will thank you. Also, you’ll get more bang for the buck by keeping the muscles under tension throughout the set.
As for the glutes, it really is in your best interest to engage them throughout the movement.
Based on your description, when you forcefully engage the glutes in conjunction with locking out the knees, you could very well be relaxing other muscles in the legs. This is your body’s way of sneaking in a mini-rest within the set. If muscles such as the vastus medialis are not contracted, they won’t be able to stabilize the knee.
This is just one piece of the puzzle. There are many others you need to be aware of if you’re going to avoid injury. It’s in your best interest to increase your knowledge base.
For now, do the following:
If something causes “wrong” pain, stop immediately and determine why that is.
Educate yourself on proper prehab work including, but not limited to, SMR, TKEs.
Do NOT make the mistake of thinking that the traditional squat is the only option. This, in my experience, has hurt just as many trainees as it has helped.
READ THAT ABOVE STATEMENT ONE MORE TIME AND ALLOW IT TO SINK IN.
One of the gyms I used to train at was frequented by a very well-known bodybuilder. In fact, pretty much every body building historian will recognize his name. He and I were talking about squats one day and he confessed to me that he can no longer perform the traditional squat anymore.
Of course there are the lucky few who are built for a lifetime of heavy traditional squatting. This bodybuilder wasn’t one them and neither are most of the lifters who consider themselves “hardcore.”
If all you do is load a heavy barbell across your back and squat for bigger and bigger numbers, you are essentially flipping a coin on your long term health. Heads you win and get to be Mr.BigDick at your gym. Tails you lose and are looking a lifetime of pain or, at the very least, reduced quality of life.