It's an issue but not a deal-breaker. Bear in mind that Terra Nova have been one of the most popular brands of lightweight tent in the UK for years, during many of which they insisted on producing only inner-first designs, and the UK's uplands are not known for being arid, and it's clear that it can be (and frequently is) made to work.
A tent is usually pitched for many hours and it only takes a few minutes to do. Even if you can't protect the inner with the flythen if it gets wet it should soon dry out with a bit of mopping and some warm bodies inside.
Pete.
