When I'm working whit web3 I have something like:
var abi = [...];
var contract = new web3.eth.Contract(abi,"0x86Fa049857E0209aa7D9e616F7eb3b3B78ECfdb0");
then I use something like:
myContract.methods.myMethod(123).call(....
In truffle test I have a contract instance in hand, and I use
instance.myMethod(123)
without the "methods" indirection, what is different from the two contract instances?