It's a difference in combo type configuration, not a quest rules setting, nor a bug.
The default new-quest template that comes with ZQuest has all the dungeon wall combo types set to "No Flying Enemies," whereas the original NES quest has their combo types set to "(None)."
It's the "No Flying Enemies" combo type that is preventing the Keese/Bats from reaching you on the top row. If you want to change that, you'll have to change all the wall combo types to "(None)." In the combo editor, change the first one, hit Ctrl+C to copy it, select all the remaining ones, hit Ctrl+V to bring up the Advanced Paste window, check the box next to "Type," and click OK to change them all at once. Just be careful to not overwrite "Overhead" combo types when you get to the door combos - you'll probably want to do those one-by-one.
So, yes, anybody starting a new quest using the default template will indeed get different behavior than the original NES quests in that regard.
I would imagine this was done with freeform dungeon design in mind. Traditional NES Dungeon room types automatically prevent enemies from moving onto the 2 combos bordering any side of the screen, but Interior room types allow them full range of motion across the entire screen, so by setting the dungeon wall combo types to "No Flying Enemies," it allows for freeform interior design while simultaneously mimicking the flying enemy limits of the original NES dungeon walls. And despite the discrepancy regarding Keese/Bats along the upper wall, I still believe it's a better option than resetting the combo types and forcing freeform interior designers to place Flag 96 (No Enemies) over all their dungeon walls throughout their entire quest, so I would hope the current combo type configuration remains the way it is (the actual dungeon wall combo layout is another story entirely).
That said, there's still another component: Link's hit box. If you go to Quest -> Graphics -> Sprites -> Link, there's a "Large Link Hit Box" checkbox on the bottom right. Enabled, Link is a full 16 pixels tall. Disabled, he's 8 pixels tall, and can walk across the top half of combos that have a solid combo above them. With a large hit box, Link won't be able to walk across the top half of the top row of floor combos in a dungeon screen, and will still take damage from Keese/Bats. However, with a small hit box, Link can walk across the top half of the top row and continue to avoid them. The original NES quest hits a compromise - a small Link hit box everywhere, except on the top of dungeon screens. To recreate this behavior, leave "Large Link Hit Box" disabled, then go to Quest -> Rules -> NES Fixes, and UNCHECK the "Freeform Dungeons" rule. Now you'll be blocked from walking across the top half of the top row of dungeon screens, but retain your standard small Link hit box everywhere else.
Of course, I'd suggest taking the default config and having some fun with freeform dungeons, but if you want strict NES rectangles and nothing else, there you go.