Front running requires pretty invasive changes to the very performance critical parts of the trading engine. You have to analyse the queued trades, decide on a trading strategy and insert new trades, all without inserting too much latency.

It would be hard (but not impossible) to implement such functionality without dozens of software engineers being very aware of it's existence and the implications.

This kind of software change only touches the edges and can be done with much more plausible deniability. The exclusion to margin calls was a single if statement inserted by a single engineer with the justification Alameda were the primary market maker. The dashboard change might have been just a bug they avoided fixing (If you normally automatically margin call negative balances, why would your dashboard bother reporting negative balances?)