This is due to apparmor_parser’s default of using all the CPUs on the system when given more than one profile. The pi3 has 4 CPUs, so apparmor will default to -j4. Setting --max-jobs=1 would make this more like processing serially (measuring the difference between fork/execs/etc). The question then becomes, for the core refresh scenario, do you want to take all the CPUs on an already constrained device? I’m guessing possibly not, but you can use the --max-jobs argument to make sure you have some overhead (eg, --max-jobs=<total CPUs - 1> or something.
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