The two at-large bids went to #9 CNU and #12 Stevenson. Union being at #13 means that they were probably in the discussion. But, Union finished the year 5-3 with only 1 ranked win (the #10 SLU win you mentioned). Otherwise, they have two losses to #1 RIT and a loss to an unranked Ithaca team. Not to mention that they also didn't make their conference championship game. Stevenson finished the year 8-1 with their only loss being against #6 York in the conference championship. They have 2 ranked wins (#6 York and #19 Stevens). They are also a host site for the tournament which means if it was close, they were getting in. CNU did have 5 losses at 11-5, but they came to #2 Salisbury (x3), #4 Lynchburg, and #16 Colorado College. On the flip side, they had wins over #4 Lynchburg, #17 Hampden-Sydney and a W&L team that was just outside the top 20.
If it really came down to it, I actually believe the spot might have went to St. Lawrence before Union. SLU had an 8-3 record, a win over #8 St. John Fisher, only losses were to #1 RIT (x2) and #13 Union and they won their conference semifinal. I think Union is a very good team, but the number of at-large teams shrinking combined with the Ithaca loss that forced them to play RIT again in the semifinal, knocked them out.