The first is he doesn't have a problem with any individual being for or against gay marriage. The second is there is a difference between an individual versus an organization (GOP Platform) having that belief.
A couple of things here.
What impact, if any, does a platform have anymore? Most often they are done with compromise and behind closed doors. The individuals all "agree" with them, supposedly, but I rarely recall anyone ever saying we are going to enact this legislation because it was in our party's platform. IMO, those have become obsolete and nothing but internal pseudo control chest thumping.
The next issue, is what relevance does a Presidents personal opinion have on a topic. I suppose the power of Veto could be used to impose their own imprint on things and they can guide legislation if they have a majority, but overall the impact is minor. The real problem arises when complete control is held by a party combined with a willingness by that party to follow that President on personal as well as political issues.