IMO what you're describing is essentially the how and why of the Meshlicious vs. the H1, and changing the factors you're describing would either make the Meshy much larger or make them essentially identical. The H1 keeps a small size through only supporting a 140mm rad and stacking its PSU above it, and keeps a small footprint for much the same reason. The Meshlicious has a larger footprint as it fits its radiator on a plane that intersects the motherboard's plane instead of "floating" above it (and supports thicker rad/fan combos). Moving the rad to a H1-like position wouldn't change much - IMO it would likely increase the size of the case compared to its current volume. Making specific affordances for cable management would also necessitate a volume increase. For the record, I've had no issues stuffing most of my PSU cables behind the PSU for a reasonably clean look. No mods or extra hardware needed, just the PSU in the outermost position. This obviously won't work with the glass side panel unless you have a PSU that can have its fan facing inwards, but it's definitely doable. I agree on the GPU cable clearance part though - either the case should come bundled with optional feet (not a fan, wouldn't look as good) or some sort of angled GPU adapter. I got some slim ADT-link adapters that work very well, but at least one should be included. It does come with an angled HDMI cable, but I use DP and that cable is way too short for my needs, so that didn't help much.
There's also the issue of cooling, with the H1 leaving the GPU to act as a set of intake fans, which is quite sub-optimal (non-ducted fans spaced out from a side panel won't do a good job of pulling air in, and will recycle hot air), which the dual panel-mounted fans of the Meshy and the different layout solves to some degree.
Still, I think what you're ultimately saying here is just that you preferred the H1. Which is obviously fine. But asking for the Meshy to be more like the H1 in that regard ... well, then it wouldn't be the Meshy. It would be a weird H1 copy. That's both the beauty and the major annoyance of SFF cases - it's a game of a lot of compromises, always. The H1 has some great strengths - it's a good bundle, it's compact, it cools most CPUs decently, and it's well though out (hinged radiator bracket, cable management). But it also has disadvantages in overall cooling and airflow, especially GPU cooling. The Meshy is slightly larger, cools better, affords custom loop building if you want to, is more flexible. But also is less thought out as a package - it just isn't designed that way, and IMO this is an inherent binary choice; getting both wide choice/lots of flexibility and good cohesive package design is nearly impossible. And that's just a tradeoff anyone building a PC will always need to grapple with. We all have different preferences, and nothing is going to be universally the best case for everyone 
