If you think the bonnet under frame is likely to hit the carbs you need to tell someone before you invest any money in painting etc.
Ask the supplier what the problem may be.
Ask the manufacturer, BMH. link http://www.bmh-ltd.com/index.html send them your photos.
The pressing of the top skin I believe to be from the original Standard Triumph tooling but the under frame looks like a kirsite press tool item, by its puckered finish. Perhaps the tooling is worn allowing panel spring, and the frame is now too flat compared to the top skin. This can be rectified by either refurbishing the existing tools or hand working the pressed frame to give it more 'curve'. The latter would require a form jig to work in and suitable tradesmen. Heritage quality dept can check this against their NOS sample panel set for the TR6. Contact Dave Jane the man in charge of engineering at Heritage.
Be careful though, the re-investment in tooling may be too expensive and the panel may get discontinued. This will be because it is not economically viable to rectify due to low sales volumes. Return on investment is driven by accountants not car loving enthusiasts.
Would you pay an extra $500 if they re tooled the frame?
Cheers
Peter W