Yes, very important point! And although Scrivener is primarily a First Draft tool, there are already so many basic layout options included that it seems odd that proper indentation is not one of them.
Actually the same indentation rule also applies for typical scene breaks (“small” ones with a blank line and “big” ones with e.g. asterisks: * * * ): The following paragraph should not be indented either.
TromboneAl, what might help you a little bit right now is to use Compile as is and have separate types of formatting presets: one which only has Save paragraph style selected, not Include font and not Include font size. Of these you make two different ones, one called e.g. P-First which has no indent, the other one called e.g. P-Standard which has indentation. Apply P-First to all paragraphs following a chapter beginning or a scene break and P-Standard to the rest.
Then you might create other formatting presets which have “Save character attributes” including font and font size selected. E.g. create one C-Standard (for the major parts of the text body) and another one C-Thought (for thoughts, in italics likely). Apply these as you see fit. With this you can change fonts and all other character attributes using character presets and preserve your indentations.
Of course everything will be much easier once proper character and paragraph styles will be introduced to Scrivener but even then it is good practice not to mix character and paragraph settings in one style.
However, whenever you rely on manually applied formatting (using presets or, in the future, proper styles) and apply “Compile as is”, there will always be extra manual work once you start splitting or joining existing scenes. So of course the best solution would be to code these indentation rules into the Compile Settings.
I think the best way to implement proper indentation in Scrivener is to have a compile option (and hopefully editor option as well) called e.g. “No first line indents” which makes sure, that whenever a paragraph is preceded by either:
(a) a (manual) blank line
(b) a non-null separator (like “* * *” or “------” or a blank line, or …)
© a title,
then the first line should not be indented. This should cover all cases where a first line no-indent should be applied, doesn’t it?