Quick Answer: Yes. [As far as I can tell] It is acceptable to use square brackets around an ellipsis [...] to indicate that you have added the ellipsis.
Although the reasons for using square brackets and ellipses are fundamentally contradictory, the fact that you are using square brackets to add emphasis to the original quote seems an appropriate use of brackets.
Note: You should be cautious about using square brackets around an ellipses. It may be too confusing for your reader to determine what you, as the writer, added to the original quote versus what the original quote was.