I'm assuming it's for accounting reasons. Having a 1A pass means you intend to actually use the CR.
That doesn't qualify as a good reason.
I haven't taken the CR since probably January but I still buy a 1A every month. They're the same price and they both cover subway and bus, but the 1A gives me the option of taking the CR to Porter or Yawkey (or other stations) whenever it may be more convenient. Since 1A is fully accepted on Charlie but Charlie is not accepted on 1A, and they're the same price, it doesn't seem to make much sense to me to buy Charlie. The only downside is that I get a new physical card every month instead of just a new pass on my existing card.
So in practice, for people who plan for these things, 1A and Charlie are 100% fully interchangeable. But for people who don't buy monthly passes with this in mind, they're not. This distinction between 1A and Charlie only works in one direction. This is stupid, and we should accommodate people who don't buy monthly 1As. For them, paying CR fares (even on the Fairmount Line) is needlessly inconvenient and expensive.
In the ideal world, every CR train would be equipped with Charlie readers for people travelling within 1A who don't have 1A passes. But there's a cost to equipping every train with Charlie readers, both in the price of the readers themselves and the hassle of having conductors carry them around for the small percentage of people making intra-1A trips without passes. So I get why that isn't worth it. But Fairmount is a much smaller set of trains and conductors to equip, and
every trip is intra-1A. The line doesn't reach any other zones!
We have one fare system designed for intra-city trips across lines and busses, and another fare system designed for inter-city trips across zones. But then for some reason, on one of our intra-city lines, we use the system designed for inter-city trips and we don't accept the intra-city system. That makes absolutely no sense! And it could all be fixed with little more than a policy change on paper and the use of existing technology. This wouldn't require some massive undertaking.