Which is by sight surely- because children will need to know that rule and the only way is by looking at specific words?
No it's not. It is teaching them that 'e' is a way of spelling the /ee/ sound and it is, in fact, a spelling which is used in many English words. The reason it causes so much angst is that the words you cite are from the much misunderstood HFW list which tend, wrongly, to be taught as though there is something especially difficult about them. There isn't; they are just words which can be taught through the decoding and blending route just like any other word.
Ds knows his w/b/m sounds but using phonics would not work.
I suspect that you really mean that your DS knows that those letters represent the /w/, /b/ & /m/ sounds. He should also, at some stage learn that those sounds can be represented by 'u' (quick), 'bb', (rubber) and 'mm' and 'mb' (summer, comb), which is no different in principle from the fact that the /ee/ sound can be represented by 'ee', 'e', 'ea', 'i', 'ie', 'y' and 'ei'.
This learning is spread over time. The alternative spellings are introduced systematically and children given plenty of practice in using them. The HFW lists muddle this because alternative sound spellings are introduced out of sequence; often so out of sequence that children haven't even been taught the principles that a sound can be spelled more than one way and that a spellling may spell more than one sound. Of course it all looks a bit senseless and difficult if you don't understand this.
Thayt is why I dislike the HFW lists so much; they are mostly perfectly 'normal' words and easy to read and spell but the way they are often introduced at an inappropriate stage of children's learning causes more difficulties than they are worth.
There are actually very few words in the English lexicon which your children are likely to encounter in the early stages of learning to read which have completely unique & possibly bizarre seeming sound spellings. Unfortunately some of them are very useful words which children encounter in text early on, words such as 'one', 'two', 'are', 'of', 'were', &, 'who'.
Learning to read is spread out over a couple of years in most programmes, though, as I said earlier, many children show an ability to 'self teach' once they have grasped the priniciples. They will also respond well to 'incidental' phonics teaching if they encounter and unknown sound spelling. In a decent SP programme the introduction of the HFWs from the YR/1 list is spread out over that period so that children are not overfaced by them.
That is also why 'decodable' texts are used for practice, it doesn't present children with completely unknown sound spellings.
This explains it in more detail:
www.spelfabet.com.au/blog/