Boeing themselves said they plan to work on a version with an internal weapons bay Which itself says there is no weapons bay on the current version. Wether thats block 2/3/4 only Boeing knows but unless there is undisclosed developments the first versions had no weapons bay.
Most of what I have read regarding the gen 2 model currently in construction is that it is the same frame as the gen 1, with improved and militarised systems. That said the contract price for the three gen 2s was $400 million, which is a lot of money.
I note Sen Conroy's words at the time were "This funding boost will enable a focus on developing sensor and mission payloads, an integrated combat system and autonomous systems".
To your point, it's possible that Boeing have their own gen 3 prototype with missile capability being built alongside the gen 2s in secret. They would get to leverage Australian funding for the gen 2 improvements and the AI development above, and invest themselves in a larger airframe, bigger jet engine and a missile interface via their own R&D. This area would be the lower cost component and could probably come from their existing parts bin. What's the diffence in making four airframes rather than three. Perhaps the Government has agreed fund it if it works. Wouldn't be the first time for such an arrangement.
Boeing would be keen to get back in the US colaborative combat drone game and out of the dog house. Given that neither General Atomics nor Anduril are currently fielding a missile capable drone (I view Anduril as akin to a snake oil salesman), they could leapfrog them with an outcome here. Boeing if nothing else has phenominal resourcing.
I should note that the new Boeing Toowoomba drone factory is due to come online in 2027, so there remains two years of prototyping time before the mass production. That gives a lot more time for a few more generation iterations to be developed. I suspect the 2027 version(s) will be distinctly different from the 2025 platform.