Rail, tube and tram lines will still be there and graded 100 years later - after track replacements, roads are not dissimilar, reservoirs and storage caverns far longer with a turbine replacement or two. Nuclear on the other hand has a much more limited life in which to absorb those overruns.
They are still within their financial budget for this project, will maybe overshoot it by a bit in the end. But that's OK, since such a dismantling had no precedence whatsoever, and it was just an estimate and everybody knew that. They will exceed their time budget by a lot, which is also OK, since again such a dismantling had no precedence whatsoever, it doesn't really matter if this thing takes a decade longer to dismantle, and the reason they take longer than initially estimated is that they had to overcome a ton of problems nobody could have known about before and went about their work carefully and systematically. There were a lot of lessons learned from this, which should help with being faster when dismantling other nuclear plants, but and a bit cheaper (maybe at 2/3rds the cost in the future).
With BER on the other hand the date of completion did matter, both politically and economically, and the exploding time and financial budgets were a result of gross incompetence in particular from the politicians that personally kept meddling in the project (it was "prestige" project), complete failure in contractor oversight (which resulted in a ton of defects and also some corruption and embezzlement) and a completely useless project leadership (of mostly political appointments, aside from the politicians themselves, that e.g. resulted in them building that thing without working fire safety).
So the fact that they are simply simpler projects which rarely (never?) have massive overruns due to "bad project management" is a huge financial point in their favor that is rarely factored in.
Those cases don't prove that trains and plains are uneconomical.