Normally a toilet supply pipe to a stop valve that is in the bathroom, and the supply line to the toilet goes to the stop valve. When using one of those pictured supply lines, the big end goes to the toilet tank, and the narrow end goes into a 3/8 compression stop valve output.
There would be a plastic ferrule, just as you would have a metal ferule with a copper supply. The line is cut to length at the narrow end, the big end is attached to a toilet, and then the compression nut is tightened at the valve.
So in your case, is the plastic supply line going to a stop valve?
One more thing... when installing a stop valve, if you plan to use a copper or PEX riser, as pictured above, it is best to have the output of the valve point to the input of the toilet. If you plan to use a flex line, I think it is better to not have the output point to the toilet input, but maybe 30 degrees off. That way the flex line can drape the way you prefer.
PEX riser:
https://www.supplyhouse.com/Oatey-34315-12-PEX-Toilet-Riser
For flex supply lines, I would consider
https://www.plumbingsupply.com/flexes.html#megawc "WC (7/8" ballcock) x 3/8" comp" Mega-flow SUPER Water-flex™ Corrugated Stainless Steel Flexible Toilet Connectors.
