Don't worry that different themes can display one layout in different ways. Isn't that exactly the purpose of the theme, to change the design of the site?
About the theme and layout templates as a set - if you use ready-made core templates, or those written in the naming Backdrop conventions for HTML elements, or if you strictly follow the naming requirements for the HTML elements that make up the template code with the community requirements , then your theme will work with any template compatible with these requirements.
For example, the standard official header name on the Backdrop Template page is
<header class = "l-header" role = "banner" aria-label = "<? php print t ('Site header');?>">
<div class = "l-header-inner container container-fluid">
<? php print $ content ['header']; ?>
In my own template I use <header id ="header" instead of <header class = "l-header" ...
I have my own reasons for this.
But if you have, as I have, your own preferences for naming HTML elements, and that determines the CSS selectors in the theme, yes, then the theme and template are a set and can only work together.
Personally, this does not bother me, because the themes I develop are not for sale and I use only for my projects and I am facilitated by a unified technique for building HTML code in the template, which I have been accustomed to since the time of Drupal 6.