You want to assail the summary court martial (SCM) on the basis that it was headed by the commanding officer of the same regiment. According to Section 116 of the Army Act, “A summary court martial may be held by the commanding officer of any corps, department or detachment of the regular Army, and he shall alone constitute the court.”
Hence, there is no impediment in holding the court by the CO of same regiment wherein the offence was committed. The law provides that commanding officer of any corps, department or detachment can constitute the court. If he involved in the any stage of investigation, then the constitution of court by that CO would have been void. Thereafter, the entire proceedings of SCM could be set aside.
It is not clear from the facts of your case that there is any infirmity in recording of summary of evidence, framing of charges and holding guilty etc. These infirmities are important and render the proceedings void. Hence, in devoid of entire facts, I am not in position to advice for filing OA in the Armed Forces Tribunal. You should consult along with all records then I can advise whether your reinstatement is possible or not.