I found the problem of the misalignment.
The problem is that the labels get display: inline-block; from https://cdn.jsdelivr.net/npm/bootstr...tstrap.min.css.
This can be overwritten by adding display: block; in the aforementioned /includes/modules/pages/checkout_payment/jscript_square.php
.inputLabelPayment::after {display: block;content: "\A"; white-space: pre;}