I finished the game a week ago. It was cool to play ct again. I feel like the events in the new parts of the ds game are made to link some things to cc. First of all, i do believe that the sanctum is a beginning of the Dragonian Dimension, and maybe its just the start of it, there's no development or anything. The thing with the altar and the prismastones are to resemble the chrono cross, maybe some sort of ritual that would be used in the coming days of the reptites, that would lead to the chrono cross in the end. I just want to believe it but i also think that the tower (the one after the bridge that the Nu guardian builds) is also to resemble Terra tower, or some inspiration to the reptites to start to build in that kind of way since it had a place to workship their saviors, it has some importance after all. I think the development team wanted to tie up ct and cc more with these events, with some events that, with the effort and time, and the relation to nature, would become in some of the aspects shown in cc.
About Magus, I would like to see more and not just jump into conclusions yet, since it is pretty vague that maybe he may not be from the same dimension as the party, or how much time has gone since he (and his party, as he says we in the event) owned Lavos, and the possible future for him after we see him in that forest in the end. I hope a new game (as we have always prayed) come to shed some light to this.