I mean first of all can we clarify if you booked the BKK-HKT-BKK as a separate award or was it part of your itinerary?

You do realize that a SEN companion award only works if all segments of the flight are on LH integrated airlines like LH, OS, LX, LO and a few regional ones. TG certainly does not qualify for it.
That is fundamental to a SEN companion award.

So while I think the explanation given to you by LH regarding segements not flown together etc. is just rubbish, you got an even bigger problem by having TG in your itinerary unless you booked it as a separate award (which would be a waste of miles but that's a different story). That would fully justify the extra mileage deduction LH has done as your itinerary does not qualify for SEN companion award.

You can fly more sectors then your companion as a SEN as long as your companion travels his/ her sectors together with you. Back in the old days I did FRA-ZRH-BKK-SIN-BKK-ZRH-FRA while my companion flew FRA-ZRH-BKK-ZRH-FRA. All travel was on LX back in the days when they still flew BKK-SIN as an add on to the ZRH-BKK flight. That is fine and was no issue (180K miles in C = 120K + 60K back then).

What you should have done is book only WAW-ZRH-BKK-FRA-WAW on LH 6 LX and buy a ticket on BKK-HKT-BKK separately. Would have saved you a bundle of miles and a RT in eco on that route can be had for 100-150 Euro.