I recently had a similar situation (not LNR) and I submitted two on-line claims. Both claims I manually entered the entire journey with 5 legs overall, as the through ticket is via an alternative route. I attached one of the two split tickets to each claim. As there was no 'free text box' to explain I simply assumed a human eye would spot that the two tickets related to the same claim/journey. In all of the ones I have made recently there has not been the option to enter your actual journey times (only the extent of the delay suffered 15-30, 31-60 etc), nor enter your fare paid or delay repay amount expected. That was calculated instantly in some cases or as part of the behind the scenes processing in others. I think I received the correct amount as Delay Repay in due course, difficult to remember as I had a bad (or good in refund terms) autumn 2023.
The automated processes have resulted in me receiving insufficient, correct, or too much in Delay Repay!