I completely understand that there's a balance to be struck between moving the story along and having the technological aspect be 'believable' - clearly Osyraa needed to take control of the Discovery and the story had to be written to make this happen.Yup, the Discovery Writers really need someone both versed in canon and critical thinking on their team who can over ride them when they start just throwing stuff out that makes no sense within the larger setting that is Star Trek.
Ship-takeovers have always been pretty ropey affairs in Star Trek, but you'd have thought that in a thousand years there'd have been some improvements in this area. Beaming through shields, no intruder alert, the nifty programable matter controls responding to the touch of enemy combatants.