I think the best way to keep symmetry in a differential layout is to route both the positive and negative signals together at all times. We should always match the lengths and avoid splitting them up, even if it makes the route longer. If the layer usage is strict, we can still preserve symmetry by carefully planning vias and using the same number of bends and transitions on both sides.
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We prefer to plan the differential pairs early in the layout, especially when the layer usage is strict. That way, you avoid problems later. I believe you should talk to your team and set clear layer rules before starting. If you do that, you can keep both symmetry and meet design rules without a headache. It's all about communication and planning.
In our case, we try using deep n-well isolation. It helps a lot because you can keep the analog circuits more protected from the digital switching noise. You can’t avoid density in mixed-signal layouts, but with deep n-well, you give analog blocks their own little island. It might take more area, but we think it's worth it.
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