They chose to start there. The classified tech was something from the beginning. Same with the tech on board being specific to the ship. In no way did they “write themselves into a corner”. Also Janeway is completely irrelevant but also she would have completely understood. This is the woman who destroyed the Caretaker array and has sacrified ways home in order to benefit the majority. Do you honestly think she would ever even bat an eye if she found out about that tech? She’d probably be interested because she’s a scientist but then completely understand why it was shelved.