How can I get rid of these 3 PMS channels, without flattening it and losing the transparency?
For each spot channel you want to get rid of, you can:
Be sure to keep the CMYK composite channel targeted except when deleting spot channels.
Transparency is unaffected, but you will have to be careful of your layer order to maintain the appearance of the composite.
This is going to flatten layers. So if you want the transparency back, you should first create an alpha channel of the transparency. Then, after you merge the spot channels, you can load the alpha and apply a layer mask to reinstate the transparency.
Simply Command/Ctrl-Shift-Click the Channel thumbnails to load them as a selection (works the same was as Command/Ctrl-clicking to load a layers transparency as a selection), then create a new channel and remove your selection from it. You can then load that as a selection for a mask.
Basically, there's no easy way I know of to merge the spot channels and retain the transparency, so you need to plan ahead - 3 steps forward, 1 step back, to get to where you want to be essentially.