We were wondering whether ISV Apps' custom fields on standard objects would count against the org limits of organizations that download our application. Most of the sources we found online seem to indicate that our custom fields will not count. However, I read this Salesforce help article and it specifically says 
if the package uses other types of custom components, such as custom fields, they count against the relevant limits of your Salesforce edition.

https://help.salesforce.com/articleView?id=faq_distribution_installing_why_do_the_custom.htm&type=0

Is there a good practice for dealing with such problem?