To be clear, if the Chop Suppression filter activates during a signal, the Buy/Sell label will not appear and the alert will not fire off, but the diamond will paint and the color will change. That means there is chop present. You should not blindly follow the Buy/Sell indicator, but should look at macro trends (i.e. VWAP or 200 MA) and an additional momentum indicator (i.e. Stochastics or MACD) on multiple timeframes for more accurate entries.
The SuperTrend indicator alone just tells you the trend (change), and the Chop Filter just filters out signals when the market appears to be moving sideways at the point of an alert/change. To continue to get SuperTrend alerts when the Chop Filter activates, you can use the "SuperTrend Direction Change" alert as that will still work whenever the indicator paints the diamond.