I suspect that they aren't factoring in the thermodynamic limits of the engines, which when applied will lead to a limitation on T FLEX.
There are further limitations that must be applied too.
I made a small app for calculating T FLEX based on the numbers from SimBrief, and even that results in sketchy take-offs now and then so there's more to it than that.
In addition, there is at least 1 bug in the TRP N1 calculation, which is that it uses indicated altitude instead of pressure altitude, which will result in different N1 REF values than the N1 values that all performance data tables are based on.
This could result in better and also worse take-off performance (I sent a ticket about this but nothing's happened yet).
On short runways, you may want to reduce the calculated max temperature by 10 degrees or something like that to give you greater margins and consider using N1 REF instead of N1 REDU or N1 FLEX.
I would've made a proper TKOF/LDG performance calculator long ago (completely free of charge), but no one is willing to give me the data I need, so sadly that will never happen.