IMHO, the important thing is the moving in itself.
If the step counting helps to motivate you, then by all means ignore this comment, it might be fine to keep counting them for you.
Whatever gets you moving is good.
Ultimately though, push yourself, not the metrics..?
YMMV, I tend to avoid most of the fitness technobabble because every other moment of my day deeply involves in tech in some way or another and physical exercise is my little haven away from it. If it helps you, by all means.
In the context of a fitness app, it's usually the exertion part of exercise that people wanna map, so measuring heart rate instead of steps can make more sense.
Using a desk treadmill, assuming you're also working at the same time, I imagine you're not full-on running, breaking into a sweat and a fitness app might under-recognize the exercise.
That doesn't mean this exercise isn't good for you, it's just more of an endurance thing than a high intensity one like the app is designed to measure.
As for metrics, maybe the treadmill has a "distance" traveled metrics of some kind?
That might be more relevant or motivating than step count.