As for the warning, this applies to use of 10Base-T SFP on any fiber port based product. Since 10Base-T connector is physically larger then standard fiber connectors which makes it physically impossible without needing to physically break something to 'stack' these SFPs. The maximum number of 10Base-T SFP that can be used is always 50% of the available ports. The other ports can work with standard fiber based SFPs. BTW you can 'mix' top and bottom ports if you alternate, still/always with 50% of max number of ports.
As for you issue the issue with ge-0/1/1 not coming up is because (from your attachement):
Autonegotiation information:
Negotiation status: Incomplete
I also think you need to re-read your paragraph #3 as I 'think' you need to change a "work" to "not work" someplace.
BTW, why does ge-0/1/1 (not working?) configured with auto explicitly set (speed auto
while ge-0/1/0 (working?) not have it set? Auto should be default config for these to start with. Since auto is failing, are you connecting these to the exact same remote device/SFP? If not the issue could be that end, not the EX4600 side.
I would suggest you try to hard code the speed, needs to be done on BOTH ends, and see what happens. Do not hard code one side and have other on auto, not supported ever, even if works.