I am assuming that having a negative kcal count LOWER than what is needed for my weight loss goal is OK?=. Is that correct?
In the short term it is fine. The 1000kcal deficit per day for a fat loss of roughly 1kg/2lbs per week that Cronometer offers as maximum fat loss goal is generally considered the lowest safe limit. Of course that can vary a lot depending on your actual body fat, nutrition (being fat adapted and keto makes it much easier to recruit body fat for energy than a vegan diet for example) and other conditions. A very obese individual can easily function at a caloric deficit of 2000kcal per day and lose fat very fast, while a very fit and lean endurance athlete may have problems at a 250kcal daily deficit already.
At too high deficits for longer periods of time hormonal issues will occur that can lead to lots of problems (impaired sleep, grumpiness, low energy, etc) and will usually result in binge eating at some point which causes the classic yo-yo dieting. Current research suggests that it is hormonally safer and in the long term easier and more effective to completely fast on some days and then eat full maintenance or even surplus calories on other days, rather than restrict your calories equally on all days.
In this context we also have to keep in mind that the caloric goals should always be evaluated as averages over a week or so. One could for example fast on some days and overeat on other days (intermittent or alternate day fasting) and come out right on target with our caloric deficit goal for the week. Over- and undereating on individual days is perfectly fine as long we keep track of our caloric goals on the weekly (or even longer time frame) averages.
In Cronometer I prefer to use the page Trends/Nutrition Report and set the filter on "Daily Averages for last 7 days" for this rather than look at individual days.