Hello,
the CSS that You mentioned is here to make the Add to cart button align together with quantity buttons and the quantity field (the same height etc.) Without it, the result for almost all themes would look bad out of the box. I’m aware that in some cases the Add to cart button may be negatively affected, but it usually happens for themes that are very liberal in the modification of the standard WooCommerce look.
While not perfect, it is already significantly improved in comparison with early versions, where the CSS would very often be off. I adjust it based on reports and handle the issues that have a high potential to affect other users, while also trying not to break things on already compatible themes. I would need an example page to investigate the issue.
The plugin does what is needed to resize and position Add to cart, especially vertically. It also centers the button’s text.
Best regards,
Ryszard