Simplifying the sentence so we can concentrate on what really matters here...
1: While we need to [do one thing], we have to [do some other thing].
2: Where we need to [do one thing], we have to [do some other thing].
In a very contrived context1 they could mean the same, but it's so unlikely you can probably ignore that possibility. Note that while has these two relatively distinct usages...
3: While breastfeeding, you should eat two to three servings of protein each day.
4: While I agree Greece has borrowed unwisely, I think bankers are the real villains here.
In principle you could replace while in both cases with the "literal" meaning at the same time as. But by "figurative, idiomatic" extension, in #3 it actually means when [but not necessarily at other times] and in #4 it means although [the first thing is true, at the same time, so is the second].
Applying that distinction to OP's example (still slightly simplified), we see that...
5: While we need to work on X, we have to make sure Y [happens].
6: Where we need to work on X, we have to make sure Y [happens].
The default interpretation for #5 is Although we must work on X, we must also ensure Y. The only interpretation of #6 is In those situations where we need to work on X, we must also ensure Y.
1 (If you've understood the above text this is probably redundant.) Note that "needing to work on X" isn't normally a situation you might be in periodically (usually you either need to work on it or you don't - the requirement doesn't keep changing). Using while X to mean when X, at the same time as X always implies that there are other times when X doesn't apply. In OP's context, it's unlikely the writer is drawing a contrast with other times when we don't need to work on sound-spelling relationships.