@Maruyama, Sota/丸山 颯太 Thanks for your patience on this.
I have checked with Azure cognitive search engineering team on this and sharing the below.
Regarding the 16MB limit, as you are trying to use the indexer, the limit is related to the search service SKU
S1 and up support the largest size of doc and also if you want to use smaller SKUs such as basic or free then you need split the docs before ingestion.