I don't think it is strange at all; in fact, I'd go as far as to say that MMC have taken a pretty relaxed view of modifications, where as other car makers have really tightened their warranty claims process (Porsche, BMW, Mercedes for a start).
My understanding, and this isn't Morgan specific, is that if you fit a part that isn't supplied by, or approved by, the maker of the product (in this case, a vehicle), and this part causes an issue with the product, the car maker is well within their rights to deny the warranty claim. For instance, if you fit an non OEM exhaust and it causes engine issues because of increased back pressure, etc, then the engine claim would not be covered under warranty.
If you think Morgan are taking a tough stance, Porsche won't allow you to take out extended warranty if you have a non-OEM battery installed
