Legal Question in Criminal Law in California

That's unusual but legal. You need an attorney. If you cannot afford one and if you are charged with either a felony or a misdemeanor, the court will appoint one. Talk to your attorney but usually you are better off if you are charged separately.

For starters, do you really think the prosecutors and the courts are likely to cooperate and conspire together to do something 'illegal' or in violation of the rules they are supposed to be upholding??

No, separate prosecution is quite common, whether requested by DA or defendant. That's no different than separate questioning in jail, to prevent defendants from sharing stories and strategy.

When arrested or charged with any crime, the proper questions are, can you be convicted, and what can you do? Raise all possible defenses with whatever admissible and credible witnesses, evidence, facts and sympathies are available for legal arguments, for evidence suppression or other motions, or at trial. If you don't know how to represent yourself effectively against an experienced prosecutor intending to convict, then hire an attorney that does, who will try to get a dismissal, diversion program, reduction, or other decent outcome through plea bargain, or take it to trial if appropriate.

If serious about hiring counsel to help in this, and if this is in SoCal courts, feel free to contact me.