I'm fairly certain that the RA4/RA6 MCUs are little endian, because looking the S-records generated, values are arranged little endian. The part I'm a little puzzled on is the hardware registers. In the RA4M2 reference manual, section 19.2.1 shows the PODR/PDR register for GPIO. It sows PODR as the high word, and PDR as the low word. What confuses me is the offset is 0x0 for PODR, and PDR is 0x2, which is behaving more like big endian. It's working correctly, it just seems backwards from other ARMs I've dealt with that are little endian.
Yes - it's weird like that.
And there are hardware registers that run contiguously that you can't load with an LDR or LDRH, they only work with LDRB.