Dual booting elementary OS, does not boot properly after install

I'm trying to dual boot OS X and elementary OS on a Mac. I've followed e.g. these instructions. The first question is this: I have not once got the "install alongside" option so I've manually created root and swap partitions. Is there a reason for this? I believe I should get "install alongside Mac OS X"?

Anyway, the install goes through just fine with manual partitioning, but when I reboot after the install, I get the (initramfs) prompt. If I just reboot again after the (initframs) prompt I only get a black screen or the underscore blinking in the top left corner. I ran boot-repair which only resulted in grub rescue after reboot. I also tried this (the 1st answer). So the second question is how to fix this?

I'm using rEFInd. Another question is, in case I can't get it to boot properly, how do I remove the extra boot options from rEFInd that stay there also after deleting the linux partitions.