I will answer this assuming you have not got a contract and don't want to write for a current series.
It depends on what age you are writing for and what you are trying to do. If you are trying to get published as a standard text for young children you will need a series of books that have a very clear progression mapped out for the reader and the teacher. In these books words have to fit the lists (a big publisher might decide they know what these lists should be, but it is unlikely an individual could) and you have to have a reason for schools to buy your books over an established set of texts.
It is possible to supplement the lists, but only with common words students would use. (I have written some phone games where the National Curriculum lists for each age group are supplemented with extra words, such as days of the week -- these words are available to the teacher.) Otherwise, you have to stick to whatever your education authority specifies, assuming that they do specify something.
However, if you want to write a children's book that will be loved, cherished and repeated off by heart by pupils for years to come, ignore the set lists. Michael Rosen didn't consider the set lists when he wrote Going on a Bear Hunt. Each Peach Pear Plum wasn't a success because it only used a limited vocabulary. The Hungry Catepillar didn't thrill children because it followed a publisher's sentence length guidelines.
Other than Dr Seuss, who wrote some stunning works of art that excited children about reading, I am not aware of books that are consistently outstanding and yet only use limited vocabulary lists. Chip and Biff (much as the series was used by schools) just didn't excite me about the world (okay, I was an adult, but still).
My advice, and I am a teacher who buys books, would be to write a book children want others to read to them so often it is memorised. Of course you have to consider the vocabulary of the audience, but more importantly, you want to set their hearts and minds on fire -- you want to change the world for a little person, not just tick off boxes on a word list.