Why not run the HE351's with external gates?
They would be enough cheaper than a Super HX40 that it would probably offset the cost of the wastegate.
The cheapest you will find a super HX40 is probably $500-600 if you get lucky.
The HE351's can be had for $300 or so a piece and will spool better and flow as good as the Super 40 on the compressor side. Like you said though, the super 40 would probably flow a little better on the exhaust side.
Also, the smallest housing they make for an HX40 is 16cm which leaves you with a combined 32cm housing size. You could always run Hybrid HX35's, but then there really is no advantage to that over the HE351cw, and they are also harder to find and more expensive than the 351.
Eric