You will not incur any additional charges for using Patch Manager to patch the 200 EC2 instances. For the 10 on-premises instances, if you use Patch Manager to patch the operating system (and not Microsoft applications), you will not incur any additional charge.
Service quotas define the default limits for Patch Manager attributes such as the number of patch baselines per account. It does not restrict you from patching your EC2 and on-premises instances.
Could you tell me more about service quotas? Maybe if you can explain on some example.
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