This is a workaround, which divides your workflow into three-steps.
(1) Go back to your original layers, and start the Field Calculator. Add a new field using the expression you have used in the Select by attributes.
The new field can be anything, but let's assume we have just created value
field with only 0
and 1
; and 1
represents the features you have selected.

(2) Run the Minimum bounding geomtry tool in the Batch mode.
Now you can use value
field in the Field (optional, see if features should be grouped by class) and the tool will create Envelopes for both selected (1)
and un-selected (0)
.

(3) Apparently we need to remove envelopes for the un-selected
features.
Start Extract by attributes tool. value = 1
is the wanted features. Ignore Extracted (un-matching)
column.

NB. You can use Extract by attributes tool (step 3) before Minimum bounding geometry tool (step 2). Perhaps it is faster than the above workflow.