I actually noticed your point while listing out the stats - that Australia didn't play many tests against Pakistan in the 2000s decade due to a variety of reasons. I tried searching for stats of Pakistani batsmen vs Australia for a 15 year period from '96 onwards and Younis and MoYo's stats dropped even further which is why I didn't list it out. But two batsmen stood out in their records vs Australia - Saeed Anwar and Ijaz Ahmed, both having a healthy 40+ average against Aus.
As for Tendulkar and McGrath comparison, you have to take two things into factor:
In the 2000s decade, it was not Sachin who played the most tests vs Australia but actually Dravid and Laxman. This was because Sachin missed most of the Aus tour of India in 2004 when they famously won because Tendulkar was struggling with a tennis elbow injury then and many actually thought that would be the end of his career then. Similarly, McGrath missed the entire series when India toured Australia in 2003 due to injury as well, when Tendulkar was present. So in spite of playing for a long time, Sachin didn't get to face McGrath in a lot of tests as you'd expect in a career spanning 200 tests.
Even still, Tendulkar had two centuries from 9 tests (you missed Sachin's century in the boxing day test in '99). He actually has a better record in Australia vs McGrath than in India and it would actually be even better, but for the 1999 tour of Australia which was famous for two things - Sachin being a lone performer for India in the series and him getting poor decisions from Bucknor and Harper. Also both Dravid and Laxman put on the famous 376 run partnership while facing an attack of McGrath-Gillespie-Warne-Kasprowicz in Kolkata. They had Australia bowl to them alone for more than a day in the sun (104 overs) and it was an Australian side that was coming off a world record 16 successive test wins. That was as good as it gets and it was not that Laxman and Dravid scored their centuries and double centuries only vs attacks without McGrath.
Also, while Pakistani batsmen have traditionally performed better in England than Australia, it is not that they were always better than their Indian counterparts. For example, in the 2000s decade, these were the averages of the following batsmen in England:
MoYo - 65
Younis - 52
Inzy - 46
Dravid - 66
Tendulkar - 52
Ganguly - 54
Laxman - 44
Pakistan were undoubtedly great in England in the 90s winning two consecutive series but India were better in the 2000s drawing one series in '02 and winning one in '07. Now I never included Inzy in my posts above and only referred to Younis and MoYo. In fact, I actually acknowledged Inzy's century at Hobart (in that test when Langer refused to walk) in one of my earliest posts in the thread. I actually rate Inzy better than Younis and MoYo regardless of what their respective career averages indicate.