I have followed D3 baseball since my son's first year in college (2007). Over his 4-years he played a lot of conference and non-conference games. Your prospective as to the importance of conference changes. By my son's 4th year, conference was something that they had to win to get the regional selection. What became important were the games against good teams.
In talking with my son now; the important parts of his conference play was he got a chance to travel all over the south (Kentucky, Mississippi, Georgia, Arkansas, Louisiana and Texas) for conference play. However, it was the opportunity to play big games against the likes of Notre Dame and play in 2 NCAA tournaments that shape his baseball memories.
They had rivalries with certain teams (which were fun) and others were long weekends playing "poor" teams. In the end; the importance of conference was it allowed for direct way into the NCAA tournament.
Ultimately your degree is from the school, not the conference.