Mahari of Bruna writes in his responsa, section 34: “An incident occurred with Reuven, who walked bareheaded in front of ten people. One of the students came, saw this, and protested to him, but he paid no attention, and the student excommunicated Reuven. And I replied that his excommunication is valid, even though we say in the first chapter of Kiddushin (8a), ‘We said this only about Rav Kahana, who was a great man’—Rashi explains: that he did not walk bareheaded, but not everyone is held to that standard—so apparently there is no strict objection. And likewise in the chapter Kol Kitvei (118b): ‘May I receive reward, for I never walked four cubits bareheaded.’ That applies to them, who were in the Land of Israel and used to walk that way. But we, who dwell among the nations, and they go bareheaded, and this is considered following the ways of the gentiles, and one is distinguishable from them only by covering the head—therefore now this is considered like one who violates Jewish religious practice, as we say in Ketubot (72a), that a woman who goes out with her head uncovered is considered one who violates religious practice. And we find distinctive Jewish practice in differences of clothing, even in shoes and sandals, in the chapter HaKonam (59b), and in a time of persecution even the strap of a shoe is forbidden [to change] (Sanhedrin 74b). And since they protested to him and he paid no attention, he is considered an apikorus, and they excommunicated him for the sake of Heaven, and even the rabbi must observe the excommunication against him, as appears in Moed Katan. Signed: Israel of Bruna.

And by the way, I would say that this applies specifically to walking, but when it comes to sitting bareheaded there is no objection, since it is normal when sitting to ease oneself and relax. And that is also implied by the expression that he did not walk bareheaded, not that he did not sit. Likewise, ‘May I receive reward, for I never walked four cubits’ implies specifically four cubits, but not less than that, and all the more so when sitting. However, everything depends on the nature of that particular sitting situation.”

You mean “Jewish religious practice” in that sense. So what’s the question? Whether violating a custom falls into that category?
The quotation you brought needs analysis. Either a custom really is considered part of Jewish religious practice, or it’s only because they protested to him and he didn’t listen, in which case he is in the category of an apikorus, and only for that reason is he considered someone who violates Jewish religious practice.
I don’t think there is clear proof here, but the reasoning and the very term “Jewish religious practice” indicate that in clear-cut cases a custom can also fall into this category. Someone who has removed himself from the community.