For a long time, search engines have been able to see the links that point to your website. All of them! In many instances, website ranking results are being penalised by search engines that know who has been trying to trick them.
A template-based website has the advantage of cost usually, but comes with the issue of looking very similar to a lot of other websites. A customised website however offers you a unique design, tailor-made just for your company. Along with a lot of other benefits that you will only discover over time.