Aji, this kind of ranking *should be* a natural result of the way Google handles ccTLDs. Are these three domains publishing the same content? (I assume so)
Each domain will need its own independent backlink profile, and ranking will most likely be harder for the .com than the ccTLDs.
Recently there have been some odd and unstable changes in geolocated search results. Whatever that is all about (and it really isn't clear to me so far) might also have some effect in your scenario - with the .com ranking better than expected in UK or India, for instance.
Still, if the same content is available on the ccTLD for a country, I would expect the .com to be filtered out of that country's results.
The real scenario is like: - example.com with 100 pages - example.co.uk with 50% pages unique and 50% page the same content as example.com (same with ccTLDs).
Now I find it really difficult to rank .co.uk above .com for a keyword (which has duplicate content on .com and .co.uk) because of its backlink profile.
I was just wondering if search engines can provide Geo based canonical tag for each page ... even for each site do I have an option - For all countries my domain is .com, for uk my domain is .co.uk (or some different domain name), so google can pass on all the link value to the .co.uk for uk based ranking ....
I am sure it will happen eventually but I don't see any such options now.
so google can pass on all the link value to the .co.uk for uk based ranking
It's a different domain, so that's not likely to happen this decade. A link to one domain is not going to pass juice to a different domain. To a company, it may all be one "online presence" but technically it is still a different website.
You've pointed out one advantage to using separate directories for separate countries, but hosting them all on one main domain. In that scenario you can have separate geo-targeting for separate directories.
That's quite an article. At the end they say "We realize this can be a little complicated". That's for sure!
Given how even relatively simple things sometimes seem to confuse Google rankings, I don't know that I'd be comfortable using that maze of rel="canonical', rel="alternate", 301 redirect, user preference cookies plus an hreflang attribute.
Joining this discussion late, but I'm in a nearly identical situation as Aji, with sites targeting the US (.com) and Australia (.com.au). Would be interested to hear if you've learned anything more about implementing the rel alternate tags since your last posts to this thread in October.