Because you have four tables establishing the hierarchy you can simply join all of the elements directly:
ON level2.key2 = level1.key2
ON level3.key3 = level2.key3
You are probably using a method to return data which needs unique column names, for example because it uses the column names as keys in a hash. You can add aliases to make the column names unique.
This is the first line of your query with aliases:
SELECT certifications.*, users.name as user_name, company.name as company_name, certstype.name as ...