From reading this motion, it looks like (1) they are trying to get the statements made at the house thrown out, as well as the statements made at Universal, and (2) the handcuffing was prior to the statements made at the house, and many many hours prior to the statements made at Universal.
IIRC Yuri's arrest affidavit made no mention of handcuffing, which is why we didn't know about it (except from Casey's text to Tony about the 10-minute handcuffing). So the handcuffing episode probably happened while the original officers were there. Would Casey reasonably have felt she was "in custody"--i.e., not free to go--while being questioned later by Yuri? I don't think so. I think she felt like she had matters well in hand at that point. But I don't know how much time had passed since the handcuffing, what explanation was provided for the handcuffing and/or for the removal of handcuffs, etc.
At Universal, though, I still tend to think she was "in custody" for the conference room interview, even if she was never handcuffed. I think Yuri and his partner knew that it would be a close question whether she was "in custody" or not, and that's why they made a big deal about the door being unlocked. Yuri had already told George that Casey might not be coming home, and does anyone really think he would have let her stand up and walk out of the building at that point, based on the evidence he already had against her?
IMO Yuri and his partner decided not to give Miranda warnings because they were hoping that they could get Casey to tell the truth. If they could, then they might not be able to use her statements against her, but they could still use whatever evidence they found based on following up on what she said. It was a strategic decision, and I'm not saying it was a bad strategy. It just didn't work, because it turned out that Casey was not just a scared young mother who made a mistake--she was a pathological and emotionless liar.