The insinuation of a pro-Gatineau, anti-Ottawa NCC conspiracy is, erm, interesting
I think it's a combination of factors. One is definitely that the times have changed, even since 2014. The NCC's leadership and its overseeing government are both much less hostile than they were under Kristmanson and the Harper government. Nussbaum and the Liberal government have seen the NCC steer quickly more pro-urban and pro-transit in a number of their projects.
There two projects are also radically different. They share the same vehicles and purpose, but is meant to carry trains at high speeds requiring a fully fenced-off right-of-way, and the other will run at 20-30 km/h with no separation. It was definitely rich of the NCC to bring up the argument considering they operate a highway not metres away, but it's also hard to make the argument that the railway-style LRT tracks would have improved the landscape either.
That actually brings me to the final reason why I think the NCC is more bullish on the tram option; the NCC likely sees it as a vehicle for radically improving the landscape. From their submission, it's clear that they're less interested in the transportation aspect and far more intrigued by the prospect of being able to completely refresh Confederation Boulevard in its look and function. Not only can they get rid of the tourist buses, SUVs, and tractor-trailers running in front of Parliament, but they'd get hundreds of millions of dollars to re-do the somewhat tired-looking boulevard for the first time in almost half a century. They'd probably love it more if the trams weren't there, but they know that they wouldn't get the opportunity nor the financial means without the transit component.
All that being true, I still think that burying LRT on the parkway was a bad move. But it's a bit misleading to automatically equate the two projects on the basis that they both have tracks.