There are three situations where applying one of the exceptions doesn't "lock in" the first vowel sound. You should explain these to your child as they are encountered. The first two involve the First Exception, that is, adding a doubled consonant to the preceding chunk, and the third, though similar to the first situation, involves the Second Exception. There are also two coding issues, one involving compound words, the other involving the concept of making a "perfect pronunciation" for spelling purposes.
Decoding Chunks Ending in "oll" or "all"
The first situation involves the doubled "l." While words like dollar and holler, and mallard and challenge do "lock in" the first vowel sound (doll ar, holl er, mall ard, chall enge) when the phonogram ll is added to the first chunk, your child will also encounter words like roller and tallest where the second sound of the phonogram o occurs in roll er and the third sound of the phonogram a appears in tall est. Just make sure that your child is aware that this happens in a few instances. He will already be somewhat accustomed to it because he will have encountered one-syllable words like roll and fall so it's not a huge issue.
Decoding Words Beginning with a Schwa
The second situation occurs with words like accuse and occur that have the phonograms a or o representing schwa sounds in the first chunk. As already discussed, adding the doubled consonant does make the chunks more awkward to blend. (It's more awkward to say rabb it than ra bbit, for example.) Combine that with the schwa sound in the chunk and the words might become difficult to decode. This issue arises far more often when the first phonogram is a, as you can see by going to a dictionary and looking up words that start "abb...," "acc...," "add...," "aff...," etc.
For example, you have words like annual and annex that decode easily (ann u al, ann ex), but then you also have words like annoy and announce where decoding as tougher (ann oy, ann ounce). The preferred way to treat these is to make your child aware of the situation, but then have him code them as having their first sounds, rather than their third. This is done strictly for spelling, in that it enables him to form a perfect pronunciation for both a and o that distinguishes one from the other. In addition, the fact that he is saying, for example, ann oy, instead of a nnoy, is a strong signal that there is a doubled consonant ending the first chunk, because if there wasn't, he'd have chunked it as a noy.
Decoding Chunks Ending with al and ol
The third situation occurs with words like falter and golden, that is, when the phonograms a and o are followed by the /l/ sound, but this time when spelled with a single phonogram l, rather than the doubled ll discussed above. Following the Second Exception (the "Hard to say" exception), falter should be chunked fal ter and golden should be chunked gol den because in both cases stopping after the vowel sound would make the next chunk, lter or lden, "hard to say." But, as with the first situation described above, the phonogram a when followed by the phonogram l often represents its third sound (al ter, al der, al so) and the phonogram o often represents its second sound (ol der, hol ster, mol dy) when chunked according to the Second Exception. Again, this isn't a huge issue, but you should be aware of it when applying the Second Exception.
Recoding Compound Words
Although not a pronunciation issue, be aware that when coding compound words like houseboat, sailboat, skyline, cannot, upon, without, and bathroom, the chunks should just be the component words. Most of them, like house boat and sail boat, for example, end up chunked into their component words just by following the Main Rule and the Three Exceptions. However, following the procedure properly yields cann ot, u pon, wi thout, and ba throom. While your child can indeed decode all four of these examples by chunking them that way, they should be recoded as can not, up on, with out, and bath room so that the words within the words are obvious.
Recoding for Perfect Pronunciation
And finally, your child should employ the perfect pronunciation technique for words that end in age, ant, ance and able by coding the vowel sound so that it helps him remember how to spell them. All of these endings are coded with a 3 over the phonogram a, but your child might prefer to code distance as di stance, indicating the first sound of phonogram a, to rhyme it with dance, for example. Or he might code cabbage as cabb age (with a 2 above the g) to rhyme it with age. But whatever he decides, he should then be consistent thereafter when coding those particular suffixes. The point is to form a "perfect pronunciation" of schwa sounds whenever spelling certain words, so that the exact spellings are more easily recalled later.
This concludes the discussion of modifications that I would make to the curriculum described in The Writing Road to Reading if I were to use it in a homeschooling environment. If you decide to try it, the next section goes through the Step by Step Instructions for actually implementing the modifications.