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The manual mentions a graphics card holder, which only works if the card is not wider than 35mm. But what if the card is taller than 121mm? Does the holder still fit in that case? The Techspot review doesn't appear to use it.
What's wrong with a plastic mount/standoffs/spacers for the drives? You can't see those unless you open the case, and reliability is hardly a concern in this case.
Personally, I don't need the front audio ports, I've never used them. However, I believe I recall a few users being vocal about their removal in the past.
As for the logo, it's up to you. A nice looking logo wouldn't hurt the overall appearance, though.
There should be some restrictions, absolutely (e.g. no Classified cards...). But having one-two third-party options would be nice.
On a side note, the additional spacing for PCIe connectors and the clips is about the same, so if they don't overlap, then it should help set the limit.
Also, I...
Personally I would rather make the chassis a couple of millimeters larger (if side panel clips require that) to retain the compatibility with third-party cooling solutions from ASUS/MSI since they often provide superior temperatures and acoustics.
GPU is the most important part of a gaming...
Uh, it only adds 0.2672 L (8.8176 -> 9.0848). Double-check your math.
I would also prefer to stay as small as possible since I don't see any real benefit from hard riser, though.
A few dollar difference is not a major concern.