I think one of the main reasons is that many apps such as banking or drm-protected apps, which are usually only offered through the official app stores, will refuse to work on a rooted or custom imaged phone. You'd have to go through youtube tutorials and have to download the software through third-party mirrors, and that's not a feature that will sell phones.
Another reason is that giving users the option to root and unlock is possible only after ditching whatever agremeent is in place with Google. So, no Play support for this vendor at all means no sales to normal markets.
Going deeper in conspiracy theories, Google would drop Qualcomm/Mediatek from the ecosystem if they'll ever allow a single SoC licensee to do such phone.
