The number of possibilities is endless, and there is no "best" setup for all situations. With 2 hAP-ac2's you have 4 radio's. (each radio has 2 streams/chains/antenna, doubling the throughput if connected to another 2x2 device, but chains cannot do different functions at the same time).
On the other hand, you are in one interference domain. Even if the signal is too weak to be used, the co-channel interference goes 4 times further than the weakest usable signal goes.
This means that independent of the number of radio's , the number of non-overlapping channels used is important. The channel width choices depend on the neighborhood interference. Normally 2.4 GHz is crowded and the free use of 40MHz wide channels is seldom possible. The only non-overlapping channels are 1-6-11 (FCC regulation and 'no_country_set') , or 1-5-9-13 if channel 13 can be used in your region and no "b" mode is used. In the 5 GHz band 40 MHz width is mostly used as minimum, but 80 MHz is no exception if enough channels are free.
With wifi-connected hAP ac2, there is one common channel for both AP functions and for the interconnect. (One and the same channel is used for clients on hAP1, interconnect, and for clients on hAP2, unless the clients are not allowed in the setup). That "one and the same channel" is a potential bottleneck !
The other 2 radio's are free and should use different non-overlapping channels. (SSID and security can be equal or not, this does not matter at all. With same SSID and security roaming of the clients will work.)
So it all depends, but for a typical case it would tend to reconsider following things in your setup.
Router:
/interface wireless
set [ find default-name=wlan1 ] band=2ghz-b/g/n channel-width=20/40mhz-XX \
country=no_country_set disabled=no distance=indoors frequency=auto \
frequency-mode=manual-txpower mode=ap-bridge ssid=Home \
station-roaming=enabled wireless-protocol=802.11
set [ find default-name=wlan2 ] band=5ghz-a/n/ac channel-width=\
20/40/80mhz-XXXX country=no_country_set disabled=no distance=indoors \
frequency=auto frequency-mode=manual-txpower mode=ap-bridge ssid=\
Home station-roaming=enabled wireless-protocol=802.11
.
Don't use 2ghz-b unless you support very old devices, are you sure to have 40 MHz free channel? , don't use XX this gives no control at all, use Ce or eC, set your country, don't use auto frequency as results will vary and the auto-choice is seldom optimal,
On 5 GHz don't use 5-ghz-a if not needed, don't use XXXX use Ceee or eeeC, set country, don't use auto frequency
"Repeater"/Bridged:
/interface wireless
set [ find default-name=wlan1 ] antenna-gain=0 band=2ghz-b/g/n channel-width=\
20/40mhz-XX country=no_country_set disabled=no frequency=2442 \
frequency-mode=manual-txpower mode=station-bridge security-profile=\
wlan1-repeater ssid=Home station-roaming=enabled
set [ find default-name=wlan2 ] antenna-gain=0 band=5ghz-a/n/ac \
channel-width=20/40/80mhz-XXXX country=no_country_set disabled=no \
frequency-mode=manual-txpower mode=station-bridge security-profile=\
wlan2-repeater ssid=Home station-roaming=enabled
add disabled=no mac-address=6E:3B:6B:86:23:A6 master-interface=wlan2 name=\
wlan3 security-profile=wlan2-repeater ssid=Home \
station-roaming=enabled
add disabled=no mac-address=6E:3B:6B:86:23:A7 master-interface=wlan1 name=\
wlan4 security-profile=wlan1-repeater ssid=Home \
station-roaming=enabled
Antenna-gain-0 is illegal, don't use 2GHz-b, (check 40 MHz width, don't use XX, frequency is odd channel, but all this is not used when it is "station-bridge"), set country, don't use station-roaming if there is only one AP to connect to.
5 GHz idem. Most channel settings are not used when used as "station-bridge" but follows the AP. But still, antenna-gain=0 is illegal,
Reconsider which one (WLAN1 or WLAN2) will be used as "station-bridge". Try to use 3 different channels in total if the RF spectrum is free for this.