The inputs it uses to spit out probabilities is known to be bad. Any scientist or researcher who claimed to get valid results from known bad inputs would be ridiculed.
To offer a concrete example here, survery respondents are often biased based on who actually sees and fills out a survey. A common technique used to overcome this non-representative sample is called post-stratification. There are, of course, limits to post stratification especially in instances of low sample sizes, but techniques to overcome issues with data are well known.
Science does not require an unbiased sample from a normal distribution to work. Bias is a technical term that the field of statistics is very comfortable working with. Scientists can also often get good results out of biased inputs.
538 has corrections for bias already. They seem to have worked in this instance - I repeat myself but: massive surprise, Biden still president.
You are pointing at evidence that 538 correctly called 11/12 races using statistics, and their confident call on a Biden president withstood a 4-7% swing (!!).
The existence of bias doesn't invalidate their predictions. Everyone knows that polls can be badly off target in a biased way - that isn't a new phenomenon.
When they talk about X% chance of Y being president they should be optimising to the outcome, not the margins.