There is no real perfect solution.
The long exposure approach is essentially the only technique that will blend the individual frames together without problems, since each of the individual frames has the motion blurred to the extent that they will blend and stitch together very nicely (the details have essentially been removed).
The stitching utility will also matter. The free ones will always have problems (MS ICE is no longer available, and probably would not solve the problems). LR and PS will work better to varying degrees, especially PS where you might be able to blend the scenes manually using translucent layers.
However, probably the best stitching utility currently is PTGui, which will afford you some additional manual control via masking to move the stitches around (thereby being able to select the specific content of each frame to use within the resulting image). Also, I would suggest using PTGui's exposure blending option - that should help a great deal. A person over on PTGui's forum suggested stitching, but when saving - export via the PhotoShop large format option, and within the export panel, specify that within the PS format, to preserve the layering - i.e., export with layers. In this respect you will then import the file into PS, but import the image file as a smart object (which will preserve both the layers intact but aligned, and allow you to perform additional post processing on each layer). You can then blend various area adjusting the amount of layer transparency of each layer to try to additionally blend the two water/wave areas together. You can also additionally blur areas with the various available tools.
An additional capability within PTGui is its ability to stitch individual images taken with different focal lengths. As others have indicated, you could then shoot the water features with a wide angle lens, and the landscape or other elements with other focal lengths to capture the details. In this way you would be removing the interaction of the wave patterns on the water.
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A Scottsman down in New Zealand shoots landscapes (lots of water and beaches) with his 645Z using stitched panoramas with longer focal lengths for additional detail. Then printing the images very large with excellent detail and colors as fine art prints. He uses the long exposure approach to perfectly blend the water details across frames. He has a youtube channel - Ewan Dunsmuir Images and has his own website. He has not really provided how he stitches, but with the long exposures, I doubt that he has to do anything special.
Last edited by interested_observer; 05-12-2021 at 10:03 AM.