Chapter encode quality differs from full-length qualtiy

[Selur]

Why would this be happening?

Bit rate control didn't have enough bit rate to spare.

Wild gueses, since you didn't share encoder and the settings you use:
Use 1pass crf (or similar) in no case use 1pass abr/cbr/vbr. In 2pass encoding this could happen if the encoder would be able to 'borrow' bit rate from another nearby scene otherwise.