Technically, the 4.6L has a 3.55" bore, and a 3.54" stroke. As far as it's high rpm application, I fail to see how it's an issue. Maybe it's an issue in a motorcycle engine where you can exceed 15,000rpms, but not in a car engine that rarely exceeds 7,000rpm. Long stroke motorcycle engines are stable in excess of 10,000rpms in many cases. The FZR 600 has a long stroke for a sportbike, and it's redline is 11,500.
Getting 20-30k out of an engine isn't favorable to car owners, neither is the fuel economy associated with running at 6000rpms down the freeway, nor lack of power in normal driving. Another issue is simply engine size when in a V configuration. On a wide 4.6L, increasing the bore by 1/2" would make the block even wider. You only have so much engine bay to wedge it in.
The 4.6L SOHC or DOHC engines will both outrev the short stroke pushrod 5.0's they replace due to valvetrain issues.
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