In a nutshell, the original question concerned whether or not it was possible for a single core to be observed running at 200% busy, as reported by Linux top, when HT is enabled.
This question is an old canard (well, "old" for multicore technology). I call it the "Missing MIPS" paradox. Regarding the question, "Is it really possible for a single core to be 200% busy?" the short answer is: never! So, you are quite right to be highly suspicious and confused.
You don't say which make of processor is running on your hardware platform, but I'll guess Intel. Very briefly, the OS (Linux in your case) is being lied to. Each core has 2 registers where inbound threads are stored for processing. Intel calls these AS (Architectural State) registers. With HT *disabled*, the OS only sees a single AS register as being available. In that case, the mapping between state registers and cores is 1:1. The idea behind HT is to allow a different application thread to run when the currently running app stalls; due to branch misprediction, bubbles in the pipeline, etc. To make that possible, there has to be another port or AS register. That register becomes visible to the OS when HT is enabled. However, the OS (and all the way up the food chain to whatever perf tools you are using) now thinks twice the processor capacity is available, i.e., 100% CPU at each AS port.