There is no problem with using a custom theme. All of the mods are designed to work with the default WHMCS themes. A couple require you to add a few files to the template, and some require edits to existing WHMCS files. Check the install docs for each mod, specifically the templates, expert and tips& tricks tabs. If you follow the documentation, adding a custom theme is not a problem
Automation here, automation there, automation everywhere! The new v4 Modules will mark a before and after for selling, provisioning, and managing Products / Services with ResellerClub, NetEarthone and many others using the biggest reseller platform LogicBoxes / OrderBox in the domain and hosting Industry.