We know the Hyksos worshipped Ba'al Zephon (who they conflated with Seth) from the big temple to Seth at Avaris and various finds relating to this form of Seth being 'Lord of Avaris'. The temple to Seth was actually maintained by the Egyptians even after they'd taken Avaris from the Hyksos.
If Avaris is meant by the Exodus writer, then you'd kind of wonder why he forgot to mention that it was a major centre for trade in Egypt. That was it's defining feature - it's position on the Nile allowing for Mediterranean sea trade (lots of Minoan influences in buildings there, pottery from Cyprus) and access to the land trade routes into Canaan and beyond. There's some debate still whether old Avaris became the main military harbour for the later city of Ramesses. But regardless, there is the slight problem that Avaris was already a trade hub 200 years before the Hyksos 'invasion'... (settlement dating to Amenemhat II at least, who is recorded as heading into Syria and capturing Aamu (Asiatics - same term used for Hyksos) as slaves).
I can buy the idea of a much later origin myth being built upon vague memories of historical events, even to the extent of the chronology becoming very confused.