I have another follow-up from this question. Although the LIKE pattern search (because of the collation set) uses the index and is much faster than LIKE BINARY, doing an explain over both of the queries seems to say that both queries use the index.
explain select count(*) from TransactionApp_transactions where merchantId like 'VCARD000%'
| id | select_type | table | type | possible_keys | key | key_len | ref | rows | Extra |
+----+-------------+-----------------------------+-------+--------------------------------------+--------------------------------------+---------+------+----------+--------------------------+
| 1 | SIMPLE | TransactionApp_transactions | range | TransactionApp_transactions_fc3e7169 | TransactionApp_transactions_fc3e7169 | 767 | NULL | 12906834 | Using where; Using index |
And I get the exact same EXPLAIN output for explain select count(*) from TransactionApp_transactions where merchantId like binary 'VCARD000%'; (with the rows being a slightly smaller number)
The key column contains the index name for both EXPLAIN outputs, but the LIKE BINARY takes 26 seconds, compared to just 2 seconds for the simple LIKE.