Given that video cables generally have the biggest connectors on a PC (displayport in particular, but also HDMI) that point is moot - the motherboard I/O not being there doesn't change the need for cable clearance below the case. And extending it to the rear always is a mess - either you implement a fixed set of extensions, limiting compatibility with GPUs with varying I/O, or you make some sort of modular system which both increases cost (requires more bundled extensions for compatibility) and complexity (requires a system for attaching and removing the rear connectors). As for the centre of gravity not moving much, that doesn't mean that it won't move, and any upwards shift for a case with a rectangular base will increase instability (a square base like the NZXT H1 is inherently more stable). Besides, the PSU is likely the single densest component in the PC, so moving it above the motherboard constitutes a major shift in the centre of gravity no matter what.
There are absolutely arguments for doing it this way, but there are IMO better arguments for not doing so. Top I/O is overall a good compromise.