Hi,
1. The fact that URLs will be different when coming from different sources is inherant to how the SEF URLs are constructed in Joomla.
To circumvent that, you can enter the URL you want to be always used in the "canonical URL" field of your category and set the "force canonical URLs on listings" setting of the HikaShop configuration to "Use canonical URL if specified". That way, it will always be that URL that will be used.
2. Regarding the template: This means that this template has custom overrides for the different view files of the frontend of HikaShop. These overrides were made based on the view files of HikaShop 2.x and the template provider didn't want to migrate the overrides to the new versions of HikaShop 3.x.
So if you try to use that template with HikaShop 3.x, you'll probably end up with many display issues and things not working on the frontend. To avoid that, you could potentially disable the overrides to use the default look of HikaShop but even then, it's possible that some code directly in the template might not work with the new ways HikaShop 3.x work.
So if you want to use HikaShop 3.x, it's best not to use that template.