Oscar...in looking at the form, I think the key is the fact that it asks you what position you served in. Unless you can put down legitimately that you served as master...I don't think you should submit the form with your own signature as master.
Acting as master at customs as a convenience to the owner does not constitute BEING the master. Were your daily duties on board those of a master or a mate...regardless of the job title you were given? That I think is the key to submitting this form. If you can say that on a full time basis you acted as master of the vessel DURING THE SEA TIME CLAIMED...then I would think all would be well. If you served as master during SOME of the sea time, I would only submit the form with your own signature as master for THAT sea time.
For example...if you moved the boat without the owner on board...you may still have been the mate...but clearly you were the master in that situation. Hope tis helps a bit.