Hi,
The PHP shortcode is to be used within the theme files directly, it is mostly for developers, that won’t help in this case.
I understand, but the alignment is hugely dependent on the container elements and their styling. All the plugin does is, it prints out the search bar where you place the shortcode. If there are other CSS rules that may conflict, the cannot be affected by the plugin preemptively, that is much more complicated than that.
If you want, you can put the shortcode there, I will take a look where the margin/padding is coming from via the browser debug tools. In most cases it is completely unrelated to the plugin. Please make sure to pinpoint where the extra margin/padding is, as I might not be as familiar with the original layout. In most cases, using some custom CSS can patch anything. Thank you very much!