That note is meant for initial stack configuration. Once you have the stack configured, you can enable LACP link aggregates for the uplink. You should create the aggregate before connecting the second uplink though.
I'm in a similar situation - I have 4x MS210s in a stack and I'm trying to figure out how to connect the stack to 2x MX100s in HA. Like @StormTrooper I read the Physical Stacking guide and assumed that you need a single uplink from the stack. However, reading the HA guide, for a fully redundant switch stack it says you need to run a cable from each switch in the stack to each MX. So my question is with 4 switches in the stack, do I need to run a cable from all 4 to both MXs (ie a total of 8 cables between the stack and the MXs)?
We have an MX HA pair at each site and a stack of physical switches that they connect to. We cable one MX to one switch and the other MX to one of the other switches. Therefore if either MX fails you still have a connection to the switch stack. Equally if the switch connected to the active MX fails, the other MX takes over and as it is linked to a remaining working switch, you still have a connection. Worst case where you get a partial failure on a switch, as the MXs are connected to the dashboard via the WAN ports, you can force a failover.