it can be done yes
but not in the standard way of using the normal commands
eg
SetFlagSide
setFlagOwner
You could do it by having a trigger over every flag.
This would be a repeating trigger, activated by anybody
(Other options are to attach an addaction to a flag and run scripts from that)
Basically you would not be setting a side to the flag and the flag would not be lowered etc, just a flag texture change and a customised scoring system.
To cap the flag, you would simply have to be in the trigger area, with no enemies present for the "Captime"
A script would then run for each flag and it would monitor the count of units on each given side within the trigger area, setting the flags texture and changing the score when the conditions are met
the following is a basic system, used to monitor the units within the trigger area named "AtFlag1"
#START
~1
?(WEST countside list AtFlag1 > 0)&&(EAST countside list AtFlag1 ==0)&&(RESISTANCE countside list AtFlag1==0):Goto "WSTART"
?(WEST countside list AtFlag1 == 0)&&(EAST countside list AtFlag1 > 0)&&(RESISTANCE countside list AtFlag1==0):Goto "ESTART"
?(WEST countside list AtFlag1 == 0)&&(EAST countside list AtFlag1 ==0)&&(RESISTANCE countside list AtFlag1 >0):Goto "RSTART"
Goto "START"
The rest is up to you.
If you want some insight into how to do a full system, then adapt the 2 way Progressive C&H system templates that ECL use.
This will then give u a choice of a standard c&h 3 way but also a progressive C&H 3 way