You could always reposition those links and render them different but the modern strategy is to supplement any sidewide links with contextual on-site links.
An example, say you are an SEO firm and you did SEO for a pesticide company. In the header or footer if you have something like:
Content Strategy and SEO London by
SEO Active
By being strategic, the sitewide link would be "SEO Active" linking to your domain SEOactive.com etc. However the
SEO and
Content Strategy Part would link internally to two pages like "jopesticide.com/seo-london" and "jopesticide.com/content-strategy".
Essentially, you have sitewide pagerank flow to these two contextual pages on a clients site whilst the main volume of backlinks are simple authority/branding which don't raise a flag with Google.
Your contextualized back link snippet on the footer or header of Jo Pesticide would be something like this:
Code:
<a href="/content-strategy" title="Content Strategy by SEO Active" itemscope itemtype="http://schema.org/ProfessionalService" itemprop="url">Content Strategy</a> and <a href="/seo-london" itemscope itemprop itemtype="http://schema.org/ProfessionalService" itemprop="url">SEO London</a> by <a href="http://seoactive.com" itemscope itemtype="http://schema.org/Organization" itemprop="url" itemprop="name">SEO Active</a>
On the landing pages, ensure that your contextual links for your target pages / website are above the fold and authoritative (H1 if possible, H2 if necessary with the anchor).
Each landing page should have some kind of side bar with LSI terms selling your Professional Service, all linking back to the parent landign page (so a silo structure / mini internal link wheel).
This way the back links for your
targetted terms get context whilst you can also piggy back page rank flow/authority by linking to your brand. This is just one specific example however if you apply yourself there's many twists to this method to ensure you are maximizing your juice.