The resistance business was something Mark had to clear out sooner or later. With Alan with him, he had to make it a priority. The teen was still not accepted by the resistance and it might have put Mark on thin ice as well.
But he could not help feel this to be the right step. The suspicions would clear out soon enough and Alan was a big enough bargaining chip. If nothing else, he could even pain this experience as a tragic sob story to gain more sympathetic points with weaker hearted members of the resistance.
"Good, then here is what you need not tell the other" from Zeno's behaviour it was clear to see that the other was on edge but he at least believe the story Mark had painted for him.
Mark could only make an educated guess that Zeno had been given a prototype shot before things had begun and had been affected. Shiro should be somewhere near the end days when rebellion had been built.