You answered the first question in the second part: if companies don't deduce pension and healthcare costs from employee wages, those wages will remain higher and make for far better statistics.
The same is true to CEO wages. You can reduce a CEO's official wage (not the absolute one) by adding pensions, healthcare, insurance, etc. Things they'd pay for never the less. If you do this, their overall wage will be lower and make for better statistics.
In the end, you'll be able to say that the wage gap is smaller between employees and CEOs. Is that good for a company? Yes it is, lovely advertisement. Is it true? No. Is it a lie? Technically, not a lie since when dealing with statistics they go around the problem by using terms such as 'net employee wage' or 'wage billed'. How many people will find out that it's not true? Very few.
For the second question, that I'm unsure of. Transparency seems to be a huge issue when it comes to companies nowadays. On the other hand, transparency means interference with the company on many terms. You wouldn't want stock brokers to see each and every tiny detail of your company, would you?