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I got an answer from support. The issue was that the user credentials used for the operation when applying from the console expire after ~7 hours, but IAM service role accounts have a much longer timeout, so applying the update using the service role allowed the operation to completely wait for the optimization/conversion process.
As for the re-optimization of the volumes, the AWS::EC2::Volume documentation https://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-ec2-ebs-volume.html states that a cooldown period is enforced when changing Iops, Size, or VolumeType; my reading of it is that this refers to the optimization process. I saw that the optimization was triggered when changing Iops even after successfully updating the stack to the gp3 version, so I guess that's just the behavior of CloudFormation and/or EBS.
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