This is a good discussion about branding SharePoint Online (SPO) in this Microsoft Tech Community post. When you customize on your own, you risk service updates breaking your customizations. Intranet-in-a-box (IIAB) face the same challenge, but it’s their focus to anticipate & update ASAP. In other words, you’re not on your own when using Intranet-in-a-box to customize SharePoint Online. In a lot of cases, they have a good relationship with the SharePoint product group and already know what changes are coming.
Your other option is hire a SharePoint developer or two with lots of experience, who will give their full attention to changes & updates to SPO. That takes a lot of dedication on the developers part. Whereas an IIAB vendor is actively looking, planning and discussing changes and improvements. It’s their bread and butter. They are motivated by the number of customers they support. They have like-minded people around them and working with them. They have the experiences and stories from supporting multiple customers and environments.
My recommendation. Choose a good IIAB vendor for customizing SPO. Foster a good relationship with them. Work with them and give them feedback. Save yourself the pain of trying to do it on your own.