I think it’s a bad idea for a beginner to be using weightlifting shoes. In my opinion, it makes sense to develop proper mobility in the ankles first, then put on weight lifting shoes to ease the burden eventually. But right now, even those shoes aren’t enough to mask your immobility, your heels are still coming off the ground.
I believe there’s a lot of value in learning to embrace the discomfort of a deep, flat footed, full squat. When I was learning to squat, one of the best things I did was spend a lot of time, not necessarily at the gym, sitting in a full squat, with my heels on the ground. You could do this for 20 seconds at a time, a minute, 5 minutes, 10 minutes. Basically, turn it into a progression as you become more comfortable with the position. This will help tremendously when you start adding weight to the squat.
You also need to force your knees out laterally more, and open up your hips, rather than just shooting your knees forward. You can also practice this by pushing your knees out with like your elbows/arms when you’re practicing sitting in the bottom portion of the squat at home.