It looks like the change isn't from either of the two issues you listed, but rather a change in how whitespace around nested text is handled.
In 3.1.1, the <createProcedure> and <sql> tags were incorrectly including any whitespace you have around the tags in the checksum calculation, which made it easy for checksums to get changed when files are reformatted etc.
Whitespace within the text is still preserved but it is no longer significant around the text. You should only see the problem in changeSets that have text nodes with whitespace around them.
I'll add a note to the release notes about the change in behavior. I don't think we want to revert the functionality because fixed logic is correct. If you have a changeSet that has the problem, the easiest solution is to add a <validCheckSum>...</validCheckSum> tag listing the new checksum. You can also set the md5sum column in databasechangelog to null and liquibase will recompute the checksums on the next run, but that needs to be done on every database and will affect runOnChange logic you may have.
Nathan