How to make tshark/wireshark to analyze tcp flow group by interface_id

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You should be able to use a Display Filter to select the interface you want and then you can export that data as a separate capture file. Once that is done you can open e.g. two files (one with interface-id1 and another with interface-id2) so you can compare what you're seeing. This should also be possible using tshark if you prefer commandline. The reason I write "should" is because I've never actually handled a capture file with captures from multiple interfaces. Can you share your capture (or some of it)?

Currently, there isn't a solution for this; however, there is a mechanism in place that could handle it, but it will require changes to the Wireshark code before this is possible.

I don't know which version of Wireshark you're using, but at least with 2.6 or later you can enable the preference to enforce stricter conversation tracking heuristics.

The preference can be enabled via Edit -> Preferences -> Protocols -> Enable stricter conversation tracking heuristics.

As the tooltip states:

Protocols may use things like VLAN ID
or interface ID to narrow the potential
for duplicate conversations. Currently
only ICMP and ICMPv6 use this
preference to add VLAN ID to
conversation tracking

Anyway, if someone were to extend the strict_conversation_tracking_heuristics preference to include the interface ID in strict conversation tracking, the problem you're facing could be avoided. At the very least, I would recommend that you open a Wireshark Bug Report, asking for this to be implemented. I think this would be very useful.