Each candle/bar on any time based aggregation period is stamped with the start time of the bar. As you hover your mouse pointer over each candle, the time displayed in the time axis of the chart is the start time for each candle/bar.
Custom scans, watchlist columns and other tools on Thinkorswim function exactly the same way. However you need to remember that those other tools will always use the Eastern timezone. The place you can adjust the timezone on Thinkorswim is for the charts. Everything else on the platform is using Eastern timezone, regardless which timezone you have applied to your charts.
Now let's look at the specific question you included in your request:
If I hit scan at 9:30 to compare close[0]>1.1* close[1] in a 4 hour aggregation, then with which previous 4 hour candle will it compare at 9:30 am.
If you run the scan at 9:30 am, you will be within the period of the candle marked 9 am on the chart. If you reference a previous candle, it may or may not be the 5 am candle you are referencing. Some stocks do not have any trading activity in the overnight session. For stocks which have no extended hours trade data, the previous candle may very well be the last 4 hour candle of the previous regular session, which is stamped 13:00 hours.