There is no direct relationship. The "Data Connection Limit" field limits the mobile data usage for the specified period and shuts down the mobile connection when the limit is reached. The "SMS Warning" field provides the user with an indication message that the specified amount of data has been reached.
You are correct in assuming that when you specify 100000 MB for the SMS Warning, you shouldn't get a warning message every time the router uses 1.2 GB of data.
This issue has already been fixed in FW version RUT2XX_R_00.01.02.6.
You can download it from here: https://wiki.teltonika.lt/images/f/fd/RUT2XX_R_00.01.02.6_WEBUI.bin