I'm not aware of any absolute regulation re medicine bottles having to be amber although fluted does denote poison. Nevertheless i suspect the reason is that your bulk purchase is for dispensing and the 3% small bottle is sold as medicine. We used to buy 20 vol h202 in bulk and as your experience that came in clear plastic but any dispensing bottles we bought always came amber glass. Having said that many liquid medicines from manufacturers prepackaged for dispensing did come in clear just to confuse the issue.
Obviously the amber protects against UV so there may be an element of expectation that some medicines will lurk around being used over a long period whereas others get finished in short order (or dispensed promptly and stored better)

pgk

Light, particuarly the shorter wavelengths, will speed the decomposition of hydrogen peroxide so it should ideally be stored in opaque or light filtering containers. The online sellers are being cheap. If kept in a dark place it makes no difference.

Robert G8RPI.