It's not necessarily. There are a couple of reasons that people...

It doesn't matter whose day it was to speak in court. The balance is found in the interpretation of what's said.

Information I got from your summary - HWL did a great job of everything, and were very clear, while the ATO tried to walk back everything. The judge felt misled by the ATO and was taking the mickey out of the ATO.

Information I got from ChillingOut's summary - ownership and control of Select All was a consideration. The freezing order was done ex parte, which puts additional onus on the ATO and opens them up to damages later in favour of JK if they were wrong. The chronology of events was disputed between the two sides. Decision to follow.

The penalty amounts are legislated. The ATO's interpretation of the legislation and how they apply this is very well documented and completely public. These interpretations have been tried in the courts on several occasions, and are still around. You can google PS LA 2012/5 to see how they apply the law, and MT 2008/1 to see their interpretation of the legislated terms "reasonable care", "recklessness" and "intentional disregard". As these are ATO publications, if a taxpayer thinks that they haven't applied penalties in line with these publications, you can lodge an objection against the penalties. The ATO are very transparent on this.

I think pomhat's point was that last vote, ~4% of shares voted were against, but actually ~40% of shareholders voted were against. The larger shareholders are pro-JK, while the smaller shareholders were much more divided. Given the makeup of the register, that's not terribly surprising.

On the most recent vote, we know that only 2% of shares voted against, but we don't know what percentage of shareholders voted against.

It's not necessarily. There are a couple of reasons that people use tax havens like the BVI, but mostly it's for tax, for asset protection, or for privacy.
Malcolm Turnbull is a good example - he quite famously had Cayman Islands holdings... But he paid full tax in Australia (as required) on his Caymanian earnings, so while it was used politically against him, it was all above board. I'm sure JK would be arguing that as a listed entity CEO, he does this or that for privacy purposes. The danger simply comes when he earns income over there, and doesn't declare it here. There's a lot more to it than that (his structure determines where he pays what tax, and the legislation defines the relevant characteristics), but the long and short of it is that the ATO have assessed that he has underpaid ~$5m of tax in Australia and has intentionally disregarded his Australian tax obligations. He is disputing this. Make of that what you will. At the end of the day, whether you think JK has done right or wrong by shareholders on the ASX and ASIC stuff doesn't really matter here - this is all just a personal tax affair for him. All it's costing us is a bit of the CEO's time and energy.