No. The Nios® II SBT4E v9.1 does not provide the feature described in rd03282005_507.
The version 10.0 and later provide the following options under Target Connection tab in the Run Configurations or Debug Configurations settings, which can be enabled independently:
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Download ELF to selected target system
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Start processor
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Reset the selected target system
If you do not wish to upgrade your software to v10.0, you may find the feature supported in the Legacy Nios II IDE tool accessible from Windows’ Start Menu -> All Programs -> Altera -> Nios II EDS 9.1 -> Legacy Nios II Tools ->Nios II 9.1 IDE.