I believe it could just be compensating for the real problem, rich condition, caused by the carburetor jet size and needle position and the restrictive air filter box.
But a mild rich condition is no bad thing during the break-in stage, it has benefits.
I believe you need the end cap and it would be wiser to replace the bolt and just experiment with shortening the internal stinger (the small tube that goes through your muffler's end cap) to reduce the back pressure but still have some back pressure. It's a two stroke engine, it's supposed to have some back pressure.
The needle in the carb can be lowered by repositioning the C clip to the next notch up. The stock jet is usually fine for break-in stage because a little bit rich makes for better lubrication and cooling, but you might try a #68 later on, after your engine is properly broken in.
The stock air filter box is restrictive though the filter inside is not particularly effective, so that can/should be upgraded to a nice big foam filter or one of those "K&N looking" filters, so the filter doesn't restrict or choke the intake airflow.
The boost in power that you will get after break-in stage from correcting of the mild rich condition (that was good for breaking in) is presumably what capless stock muffler is mimicking. But the capless stock muffler isn't quite the right way of getting there, and it may be too soon to be running the engine leaner and hotter anyway.