If Yamantaka can be practiced by Je Tsongkhapa, of course it is excellent for the rest of us.
Nechung came to Duldzin during the time Je Tsongkhapa was alive, although Je Tsongkhapa was a pure monk and very gentle, how would a Buddha not know Duldzin was being visited by a negative force, that eventually brought about the arisal of Dorje Shudgen.
Duldzin was also reputedly to have the same level of realisations as Je tsongkhapa, could he not see what Nechung proposed would turn out to be negative? Impossible!. Je Tsongkhapa could speak to Manjushri at that time and if Duldzin was of the same level, there is no way Duldzin would agree to becoming a spirit in a future lifetime.