Yes. Remember it's essentially the same system (components, OSX, Clover, smbios, Energy Saver settings, everything), just the motherboard was changed.
Here's some evidence: (the funny time indicators are "am/pm" in greek)
Altair86:~ xenophon$ uptime
16:19 up 20 days, 6:30, 2 users, load averages: 1,09 1,33 1,35
Searching for "wake reason" in today's console logs:
13/1/16 3:51:28,000 μμ kernel[0] Wake reason: PXSX GLAN XHC
13/1/16 5:20:02,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
13/1/16 6:21:00,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
13/1/16 7:22:00,000 μμ kernel[0] Wake reason: PXSX GLAN XHC
13/1/16 10:48:41,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
13/1/16 11:49:40,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 12:50:39,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 1:51:37,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 2:52:37,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 3:53:36,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 4:45:18,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 5:46:16,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 6:47:15,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 7:48:15,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 8:49:13,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 9:50:22,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 10:52:26,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 11:53:25,000 πμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 12:54:24,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 1:55:23,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 2:56:21,000 μμ kernel[0] Wake reason: RTC PXSX (Alarm)
14/1/16 3:57:21,000 μμ kernel[0] Wake reason: PXSX GLAN XHC
Please note that:
• "Power Nap" is enabled in energy preferences
• Time Machine backups occur as expected
• some RTC alarms emanate from ChronoSync scheduled scripts performing backups in the middle of the night
• oh, lest I forget: the recipient of the backup scripts (also a former Gigabyte patient, now cured by Asus), wakes up with WOL and receives the data without incident
I hope you agree that, indeed, the GA-Z97X-SLI and H97-D3H motherboards were the culprit, at least in my case (two OSX86 setups). Current RAM DIMMs are the same as previously.