1. The court will issue bailable or non-bailable warrant only when the accused is absent without any reason and there is no representation on his behalf.
If the advocate is filing a petition under section 317 cr.p.c. to condone the absence of accused, the court may at its discretion allow the petition.
If the court has dispensed their appearance allowing a petition filed by them under section 205 cr.p.c then the accused need not appear before court until and unless the court orders their appearance.
2. Without any sufficient reason you canot seek transfer of the case to any other court. Because the reason you have stated that they have not executed bail bond or they are not appearing before court are not tenable in law because there is no violation of law in this. There is no necessity to obtain bail bond in the private complaint.
3. There is no law restricting you to make a complaint against the magistrate, but you should convince the reason for your complaint, the reasons what you have stated are not sufficient for a complaint, moreover if this backfires, then it may impact your main case itself and it may even turn fatal to your own case.
4. In the criminal complaint you cannot recover the money.
If you have strong evidence that the builder has misappropriated you money you may file a civil money recovery suit which shall be the proper relief and remedy to you
In magistrate court, if he is found guilty he may be punished with sentence of imprisonment. The criminal court cannot pass an order for recovery of your money.