Will saves be saved on physical cart?

[HeartTranquil]

If I buy the physical edition which comes with both games? What about DLC 3rd path? Will the save still be on cart?

Oh yea, do you guy recommend phy or digi for FE and did you go digi for FEA?

[Book of Ereshkigal]

Probably.

Are there even any physical 3DS games that even use the SD card for primary saves? (I'm not talking backups or anything)

I go physical all the time because I like it, though it's up to you.

[sforzur]

You can manually force it to save to the SD card if you'd like, though it'll save directly to the cartridge like every other game otherwise. The save file will probably just lock itself if you try to load it on a system that has not purchased the DLC.

I stick to digital for imports (cheaper/faster) and physical for localizations.

[VincentASM]

If it's like Awakening, the saves are always on the game card by default. Even if you have the DLC.

Although if you saved in a DLC map and load your game on a different 3DS that doesn't have the DLC, the game will complain about the DLC not being there.

I only know a few exceptions where the game saves to the SD card: Fantasy Life and Monster Hunter 4 Ultimate (unsure about the latter, since I've never played the game on my other 3DS).