The way that most of these functionalities work is they will target an entire product and not individual variants of the product to display. This means that they can pull and display the app created variants and/or their prices. Unfortunately, there isn't anything that we can directly do about that since we don't have any control how that functionality works. On the Shopify storefront we're able to hide the variants and their prices through the access that the Shopify platform allows us, but unfortunately, we don't have any such access to these third-party functionalities, and any direct change would need to come from their end.
One potential way around this issue would be to have two separate instances of the same product in the Shopify store; one for the Shopify storefront and one for these other sales channels. The storefront version will have the app's functionality applied to it and can be hidden on the other sales channels, and the other sales channel version will be hidden on the storefront and not have the app's functionality applied to it. This way the app's functionality will still be available for the product in the storefront, but the app variants and their pricing won't be showing in the alternative sales channels, and there won't be two versions of the same product showing on the storefront.
You'd be able to duplicate the pre-existing product through the Shopify admin (ensure that any app group that is targeting that product is turned off, and the app is finished removing the app variants on that product), and then set that duplicate to not show in the "online store" in the visibility settings for that product. Then you'd be able to set the original product to not be visible in the alternative sales channels and turn the app's functionality back on for it.