If your rear mounts are bad or not installed properly, including spring washers then you cant align engine properly no matter how you redesign or add pieces to the alignment tool. The mounts have to be in correctly to insure proper height of rear of engine. Then and only then can engine be aligned correctly. If you are pinning or staking rear mounts for HP setup they still have to be the same height as original mounts or it will not line up right. The alignment only aligns the coupler with the gimbal bearing on an alpha or bravo drive. The angle of the bottom, the transom or the bell housing has nothing to do with it. From the gimbal bearing to the drive the alignment changes any time you trim or turn the drive and has nothing to do with spinning the hub or splines on the coupler. When the drive goes on the U-joint shaft goes right up against the gimbal bearing and never moves between first U joint and coupler unless eng mounts are bad or loose. Hope this explains it a little better.
On the TRS drive the alignment tool with the disc that fits the bell housing is really only used to center the tail shaft of the trans to the gimbal housing while aligning eng. There is no rubber hub coupler on them and the gimbal bearing is pressed into the tailstock and shouldnt move.
No, they do not make different transom housings for different angles, at least not stock.
Ever see a drive saft on a car that was perfectly straight? U-joints are made to work at different angles.