your users should not have to install Arduino to use your product.
... It's also not an appropriate method for programming large numbers of units at your factory - there are better programmers for that...
2. The really big stuff gets their chips programmed during manufacture by ATMEL. Intermediate size needs to program batches of chips (10-100) in a big programming fixture that works on all chips simultaneously.
3. Yes and no. The Arduino is popular because the shields are relatively standardized. If you take away the pattern of headers that mate to a shield, then it's no different to starting the design from scratch.
You can order preprogrammed chips from Digikey and I'm sure other suppliers.The value of the shield compatibility really depends on the product. Personally I much prefer using Pro Mini/Pro Micro/Nano type boards and many other users feel the same. The only board I use with the Arduino header pattern is the Mega. I think just having publicly available Arduino source code and the ability to easily upload sketches via the IDE would be enough to make a product appealing to the Arduino community in many cases.
What are the native languages that are more "efficient" than Arduino?
There actually isn't an Arduino language. It's just a collection of libraries written in C and C++. If you can write more efficient code than the Arduino libraries then your code will be more efficient. If you can write better assembly than the compiler then that would probably be the most efficient but the compiler is pretty good.