I think you've picked up on my explanation, which was taken from 新完全マスター文法N3, 日本語表現文型辞典 so, as I do find the expression with は intuitive/natural, I should expand on my previous answer.
The definitions were:
によって：means to change state or behaviour depending on something or according to something. It expresses variety and is often used with さまざまだ and かえる.
によっては：pinpoints one outcome from a range of possible outcomes.
Sentences given in the book applying によって are:
One sample sentence in the N1 book pinpointing a single outcome using によっては was:
I get home at a different time every day. Some days I get even home in the middle of the night.
A similar sentence to this last sentence applying the same principles used in the first two sentences to express variety using によって would be:
The time I get home varies from day to day.
If we work backwards, taking the last last sentence as the starting point and then seek to pin point one result, taking "as for" as a crude translation of は then we would say:
Every day I get home at a different time. "As for some days, depending on the day itself", I even get home in the middle of the night.
Which takes us back to the sample sentence of によっては with what I hope is a crude but reasonable explanation of how は is used not just in this expression but in a manner that is consistent with some of its normal uses (raising/drawing attention to/ emphasising a topic)
Consider also other ～ては structures:
BによってA is used in sentences to make statements such as "A varies, depending on B".
BによってはC is used to make statements such as "As for all possible results dependent on B, C can happen", C being a member of set A.
は selects Bによって as a topic for further discourse, similar to ～については and ～に関しては.