ARC can carry Dolby Digital Plus, which is required for Atmos. But both optical and ARC carry Dolby Digital, which is a 5.1 codec, and what the majority of content is in.
The other thing you lose when using optical over ARac is CEC, the ability to carry things other than TV audio, such as volume commands, etc.
There are several TVs, especially from LG at this point, who have had issues with the firmware in the TV set not dealing with ARC properly. In some cases, new firmware has been released, in others, it appears that there is still an issue. If it were a Sonos issue, these issues would be across all TV sets, which is not the case.
You have to decide if Atmos is important to your viewing habits, and if your TV is stricken by this issue. It might be worthwhile asking your installer if s/he’d be willing to come back out at a later date and switch you from optical to ARC. Unfortunately, this can not be decided for you. You have to weigh the issues, and how they may impact you, and tell your installer what will work for you.