Hi Partner,
When you conduct a web check-in, there is an option where your boarding pass gets generated online, and you can print out the boarding pass for presenting to the airline's staff before actually boarding your flight. So, this should be fine for the LTA exemption.
Now, if one were to consider the unfortunate situation where you had checked in online but could not board the plane, then any verification of the boarding pass with the airline in the event of a tax return audit could land you in trouble, as their records would indicate a check-in but no boarding.
So, yes, as long as you have actually boarded the flight, the boarding pass generated via web check-in would be valid for LTA exemption, provided all other conditions of the LTA policy have been abided by.