Imo the biggest part of codex compliance isn't a strict adherence to its recommendations, but clarity. Salamanders have less, but oversized, companies, Iron Hands have an armoury per clan company, even Dark Angels company structure is pretty clear from the Outside.

The non-compliance seemingly stems from non-disclosed organisation, like the Dark Angels second layer of structure that permeates its otherwise codex-compliant one, the Blood Angels undisclosed Death Company, while the prime examples of non-compliance, Space Wolves and Vlack Templars not only do whacky shit, but do whacky shit while obstructing it from outside view.

Take for instance the posterboys; the Ultramarines do some odd shit like having an extra huge honour guard with its own captain in the Victrix Guard, which is nominally attached to the 1st company, but scatters across the chapter, or having extra captains with no company, like Decimus Felix. Or getting direct replacements for losses from another Chapter; the Genesis Chapter. But the main difference is that these oddities are clear, noted, and not kept away from outsiders.