A PHP version of Radiant is a port not an integration, which is very different. And neither of your reasons for my opinion apply, I just happen to think its a bad idea. Trying to closely integrate a third party code base into a structured framework like Sapphire just doesn't make sense. Monsters are bad... they get unruly and always bite the hand that feeds them!
However some well constructed bridges to other eCommerce platforms for more serious stores is a very viable option until the native Silverstripe module matures enough to tackle more ambitious projects. And yes I agree user sync is the usual stumbling block in this area, but its certainly not insurmountable.
I have looked about for active implementations of the eCommerce module and they are either very hard to find, or very thin on the ground - maybe both. Bit of a Chicken and Egg situation here. Until more people use it in anger the problems with it won't be found and corrected. Not talking about bugs here, but operational issues, like poor order management.
Anyway, three options seem likely;
A) Continue to make the native module better
B) Splice in a third party cart
C) Bridge to bigger and better eCommerce platforms, like Magento
In my opinion A and C are the way to go, others may disagree :o)