The proposed "timer bypass" nuke activation (ie. rewind 5 seconds, nuke, fast forward 5 seconds) is a neat tool in the same way replay editing is (and really, it is an example of replay editing under the hood). But some of the observable side effects (such as cases Simon mentioned) will probably look too confusing to the uninitiated to be left as the default. It feels more like an advance feature like replay editing, that may be better off only invoked on demand for those in the know. Maybe something as simple as holding Shift key while invoking nuke via any input method.
I should note that I haven't played much custom levels let alone those that require nuke solutions, my experience is heavily biased towards challenge solutions. In those cases at least, timing the nuke is often just a small part of the overall work needed to plan things out. Much more effort tends to be spent on things like planning release rate changes, timing certain skill assignments, finding certain key lemmings to divert from the overall stream, etc. Still, every little bit helps. Then again, given it literally is no more than rewind-nuke-fastforward, it is already achievable today manually; the convenience of having the sequence carried out with one keystroke is nice but not that essential.