Specifically regarding the iframe discrepancy – Jacob Peattie was right in the comments. This was caused by jetpack’s builtin blocks not being registered with version 3. Once I disabled them via Jetpack -> Settings -> Writing -> Composing and unchecking “Jetpack blocks give you the power…”, the iframe appeared as expected.
Here’s the link explaining the iframe behavior correlated with the block api version 3
My question was more broad than this specific issue, however there are probably many small incompatibilities such as this which will not all be documented in one spot. If I run into more I will post additional questions.