Assuming you have updated LR to 6.10 or 2015.10 and updated ACR plug-in to 9.10, then this is a known bug in the current version of Lightroom. You should be able to check the "do not ask again" checkbox and then click the "open any way" button and be good to go until Adobe fixes the erroneous message display.
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The first message that you get indicating that you need an update is an error. This has been confirmed by Adobe. I am by no means an expert in HDR images. I have done a few. I understand the concept. It frustrates me. I don't do it a lot. But after reading your message a few times I went into Lightroom CC 2015.10 and selected for NEF files and chose the option to merge to HDR Pro and Photoshop. I got the message that you indicated and clicked the box to open anyway. Photoshop opened as expected and Photoshop proceeded to build the HDR image. The four images were "stacked" and then HDR Pro opened and allowed me to tweak the image. When I had done all that I felt that I could in HDR Pro I clicked OK and the image opened in Photoshop. As I understand it, this is the way it should work. I have also created an HDR image in Lightroom alone, as well as in Camera Raw alone. And both of those methods seemed to work as expected. I am using the current versions of Lightroom, Photoshop and Camera Raw on a Windows 10 computer. What am I doing differently from you that I am not understanding from your workflow?
As far as the message indicating that you need to update your Camera Raw is concerned, that will be rectified in an upcoming update from Adobe.