The problem is that downtime happens all the time in many forms of content, high end or otherwise. You can get it in normal or Criterion dungeons, normal or Savage raids, Alliance raids, Ultimates...
This Savage tier had almost no downtime because it happened to be so, but it's not healthy for the game or for PCT itself if the devs cannot add downtime to fights or add it and then realize how strong it makes the job, thus being forced to nerf it without proper consideration.
PCT dealing more damage when downtime is involved is a huge boon because it's a job that it's meant to deal no damage for a specific amount of seconds in full uptime to prepare its actions. If its strengths were more niche, such as fights with two stacked targets, then it would be fine because they're quite rarer in comparison. But when the job is strong in normal fights with full uptime and extremely strong when downtime is involved, there is a potential balance problem.
The most elegant solution is to shift some damage from the burst into the filler. Ideally, the overall damage would be kept the same but the effect of downtime would be lessened.
I've seen you talk about the "gold parse" often. The max of a job is irrelevant. You could even ignore the 99 percentile as well. Just look at other percentiles from 95 and below in level 80 and 90 Ultimates and you will see PCT either dominating or very high up. Balance in old Ultimates is not relevant but it does show a trend that will be repeated if FRU is designed with plenty of downtime, as Ultimates tend to be.
Better that the devs take action on this to preserve PCT's game play than get a hasty nerf when they realize the problem.