Yes, this is a concern, but it is not as hot as the ST1300. Honda is still trying to deal with the heat issue. Depending on where you live this might not be an issue at all, but if you are dealing with severe stop-n-go traffic, then you might want to speak and maybe ride one owned by someone else (if they are amenable). But all of this set aside the last day to put down your $500 is coming up for this year's models. My son works at a motorcycle dealership and they have had no complaints with with FJR1300 customers. Customers have backed out of ST1300 deals after reading talking to some other ST1300 owners.
You might want to speak with your dealer as the FJR doesn't sit on the floor and my son tells me that others quickly step in when others leave their position. The deposit is refundable at my son's store, but he just got off the telephone with me and said that there are always several buyers who missed the deadline looking for people backing out to take their place. However, each dealer might be different and you need only look at the fine print that your dealer will have you sign before laying out $500. Here is Yamaha's basic terms (without the fine print):