Probably not – in the modern “mnemonic” type systems which break down kanji into a complete set of sub-components, the exact choice of components is going to depend on what components have already been taught at that point, what components seem to produce a memorable set of images for a mnemonic, and to some extent random whim – over 2000 items there is unlikely to be complete consistency. For these systems it doesn’t matter much whether the division happens one way or the other, as long as there’s a memorable hook between components and meaning.
One example of random inconsistency that’s been raised here before is the 空 kanji which WK breaks apart a bit differently to others with the same top half.
I suspect you’ll find this gets easier as you go on, both because you get more experience of how characters are put together, and because the simple few-strokes kanji that are taught first tend to be the ones where the split is most non-obvious – in a more complex kanji like 語 the split into three parts is clear, for example.
If you’re spending much time doing by-radical kanji lookups it’s probably a good idea to find an improved method for doing the input (eg handwriting recognition on a mobile phone) – a multi-radical search is pretty slow.