ALTLVDS_RX->LVDS serdes Link Training

In fact, that is what you want to do. Since each channel calibrates independently, it's possible for them to be off from each other. I'll admit, this is a strange thing, as I recommend doing this alignment, but I know of users who have put down DPA designs, never calibrate, and have it work. I think they are at speeds and have layouts where the DPA always aligns to the center of the same bit. Note that the DPA chooses a sampling clock for the most margin. Let's say in one channel it thinks everything is fine, but the channel next to it there are some slightly different delays, and it decided to choose a sampling clock one cycle over, in which case the bits are not aligned between channels. Sending a known patter(which most ADCs do, as far as I know) can allow you to calibrate, and would also alleviate the need for FCO.