Updating Partitioned Table with Cross Apply
In the second plan, the optimizer chooses to update one nonclustered index using a per-index strategy, while the other nonclustered index is updated per-row, at the same time as the clustered index update. Plan Explorer highlights this per-row maintenance in green.
The optimizer makes a cost-based choice whether to maintain each nonclustered index per-index or per-row. Reformulating the query in this case happened to change the cost estimates and so a different choice was made. There will not be a general correlation between the query forms and index maintenance strategies.
I wrote more about this in a recent blog post.