Hi,
Let's see it in a different point.
This plugin might be cool but it just not support things like "I display a message in a popup".
So, you can just remove this HikaShop "add to cart" notice popup which display a joomla message into (and which generates a nice cool error) or you can ask to the developer to support the fact that, in some context the best is not to override the official joomla message system.
It is clearly not complicated, just have to check the "tmpl=component" parameter and do nothing.
We are not the only extension in the world which display such message in a popup.
We use Joomla message and Joomla popup, we don't have any kind of specific implementation for it.
In our side we can't do anything and I don't think we do anything wrong too.
I am not saying that the other extension do it wrong but, for my point of view, there are some cases which are not right supported.
I don't want to be impolite or rude but I don't see want we can do for such problem and I don't want to blame for using Joomla native features.
Regards,