I agree. Having worked in technical customer service I understand the concern of an additional factor to deal with in troubleshooting. But a global CSS enable/disable toggle should handle that just fine. It could certainly result in having to make frequent first replies in customer support of “did you disable CSS and test this again?”, but that may be mitigated by an auto/intelligent response in Intercom, and a notice on the issue report function that custom CSS isn’t supported and must be disabled before making issue reports. So custom CSS as a feature does have the potential to cause some support issues, but I think they can be mitigated enough, and meanwhile the potential savings in dev and support time for minor aesthetic preference work would be minimized or removed entirely. On balance it still seems worth it to me.
And a (possibly not insignificant) bonus: Fibery would be the only major SaaS PM tool I know of that allows this! So it becomes a marketing feature as well.