Lots of lessons are to be / being learned for this FAP. While it was understandable that PN was trying to initially grope in the dark during bid definition stage, the succeeding stage 2 (via the
SBB amendments did try to address some inadequacy. Baseline established. It was perceived that a set of supposed sub-components were also included during the submission and opening of bids -- in order to established if such incorporated sub-systems were compliant with the baseline. The bone of contention lies there. Substitution could possibly lead to non-compliance, and actually -- possibly violating the procurement law.
The current US Navy FFG(X) procurement process give a valuable lesson, including those from their own 'flawed' LCS program. The platform is calling for a parent design which had been
constructed and demonstrated at sea -- rather than a
developmental design. This approach lessens the time involved in testing and debugging -- thus having the platform operational at an early date.

Another basic US procurement approach is the provision of Govt Furnished Equipment (GFE) for the platforms. PN could have had de-coupled the combat and warfare systems from the platform, so that it will have the ultimate control on which subsystems and integration it wants. Separate acquisitions with long-term and multiple platform outlook could have been done.
Monday morning quarterbacking is rather easy... But is the game really over?!