Can we modify the scripts of an installed bundle to improve it? We have a bundle that automatically creates credit memos for withholding tax upon acceptance of payment but it does not capture the related project of the invoice.

if it’s locked, there is nothing you can do except scripting on top/or after the output the bundle execution. If it’s not - you’re in luck but be mindful that your script might break if they roll out an update to the bundle (manage). For best practice, TLDR: Not a good practice.