I'm not sure if a similar post has already discussed this but I just want to share that I am able to run Pokemon Unbound (a FireRed ROM hack) with real time clock. I have seen a lot of posts saying that GBARunner2 struggles with ROM hacks like these, however, an unofficial release by therealteamplayer (link here: https://github.com/therealteamplayer/GBARunner2/releases/tag/v20210911-merges-and-tweaks) increased compatibility with these types of games. If you have the latest version of TWLMenu , this version of GBARunner2 should come with it by default. Consider updating if you haven't. I want to share how I was able to do it. Note that this only works for DSi and 3DS.

Here are the steps:

1. Download the GBARunner2 version from the link above and use that instead.
2. Prepare your ROM hack .gba file and go to this link: https://wiki.ds-homebrew.com/gbarunner2/faq, and click on the "Why isn’t RTC (Real Time Clock) supported in a ROM hack?" drop down.
3. Upload your rom hack .gba file and change your rom hack's title ID to a game that supports RTC. (Example: Pokemon Emerald Title ID: BPEE) Hit enter and then press Save to get your modified ROM.
4. Transfer your modified .gba file back to your console.
5. Launch the game and press the bottom screen to open GBARunner2 settings. Under "Emulation" Settings, tick the "Skip bios intro" setting and then save your config. This enables you to skip the BIOS bootscreen which gets stuck after modifying the game's title ID.
6. Reset GBARunner2 and now it should work.

Do note that I haven't tested this on other ROMs, and I haven't progressed in the game yet considerably. But for now, the game is running perfectly without any slowdowns, and with only a few very minor graphical glitches.

https://preview.redd.it/so9isc423wf91.jpg?width=1878&format=pjpg&auto=webp&s=61e79715cc1f1542e9d5409e4404ef59de818393