In Qlik Sense you add instructions to load and manipulate date using the Data Manager and the Data Load Editor. It can be compared to SSIS with regards that technically both perform Extract, Transform and Load actions. But SSIS is a purpose built ETL Tool. Qlik Sense is a Data Discovery tool with some built-in ETL functionality.
Qlikview/Qliksense is infinitely more "intelligent" vs SSIS.
SSIS is a "brute force" specialized ETL tool, that will not "tolerate" any change in the source metadata.
In Qlik you could select/filter/identify subsets driven by business driven conditions. It is true that the underlying data is stored in a proprietary Qlik format. However, any table/chart could be exported into excel in matter of seconds (in Qlikview even better/simpler that from Qliksense). For complicated data models, for prototype stage, Qlik is infinitely more flexible (than SSIS).
Summary: Qlik is not a specialised ETL tool, however, it can be successfully used as for ETL.