My guess is the reason for not letting people inject their code directly could be:
1. Making it easy to work with for people new to java and the dev at all - a full size IDE may be a bit intimidating for a fresh user.
2. Protecting the modules from any dangerous or troublesome code, like enforcing only one constructor with predefined body...
3. Keeping all resources in one file - again this is for the people new to java or coding at all
4. Preventing debugging tools from touching the internals of the application
There is also the benefit of the visual designer which is easier to be used for pople who are not used to code their user interfaces.
Apart from points 2 and 4 I don't see any reason why one shouldn't be allowed to use an external IDE for the whole module dev process.
Point 2. can be enforced by some code analysis build-time or reflection run-time. Code analysis requires more work but may catch any illegal code i.e. in the constructor's body.
Point 4. may be a bit diffcult but there are ahead of time compilators for java available which produce native binaries, those are harder to reverse engineer - note java classes can be investigated as soon as they are loaded into the memory, its not straight forward but also not impossible.
VM looks like a product which if well planned could be executed by a single skilled developer, there are probably more people working on the supporting infrastructure than the VM itself
Certain features may require extra people with apropriate skillset or at least some time for the current team to learn about the requred technologies... This is not something a company runing such small project can take lightly...
The point 4 could be also resolved by providing acces to extra tools ona a basis of an appropriate NDA, however maintaining a legal team which deals with any breaches may turn to be too much comparing to the benefits. Not to mention a breach may have inrevesable consequences for such project...
Anyway, after all that serius stuff being said, a way of seamless integration with a java build system would be a great addition to the feature set of the VMD