Zinal, there are three options to resolve this
1) as you do now ... eg. scrap items than don't fit (which does your fix in 0.13.2)
2) spawn aditional chest (1 or more)
3) have predefined multiple chests with different stack size
Main issue with size of chest is, when people using big inventory mod, or for example bobmods, where trough tech research and by equiping mk5 power armor you can go up to 300 slots (including trash)