Taxonomy and post type terms are required in permalinks so WP knows how to create the correct query. On certain sites which have no conflicting taxonomies or post types in use, it’s possible to remove them, but there can be no duplicate slugs between product-category and product. If WP cannot find a matching slug in the assumed default (product for example), then it could try querying the other (product-category) for a match. So in many requests, WP would need to make two queries, slowing down the site.
So yes it would slow down your site, additionally doing so is only possible in certain circumstances and would require re-working how WP works in a fundamental way.
You don’t have to use “product-category” in the permalinks though, it can be any unique string. “cat” if you wish, as in example.com/cat/clothing/. Similar for product. And as I mentioned earlier, if you do not use blog posts (the usual default post type), you could make “product” the default post type and eliminate “product” from permalinks entirely.
I’m not clear why your parent theme slug appears in permalinks at all. It is certainly used to reference theme resources like CSS files, but not in permalinks where an actual file does not exist. It’s not an actual server folder where your root WP installation resides, is it? Does it appear in your site and home URL settings?
You’re using WooCommerce plugin, correct? Its normal URL to the main store page in English would be example.com/shop/, no theme slug. “shop” is the English default, it can be anything you like. “boutique” of course is fine. The theme slug being part of it is just plain strange. Without knowing why it’s there, it’s hard to suggest how to remove it. I suggest asking in the theme’s dedicated support channel, but in this case they may not be very motivated to help.
BTW, if you were to make “product” the default post type, WP will assume a “boutique” request to be another single product and would likely go 404, not found. You’d need a special rewrite rule just for “boutique”, telling WP this is really a page and not a product. I hope you can now better understand why you cannot have just any permalink structure you want. WP needs enough information to create the proper query without having to make extra queries trying to guess at the user’s intent.