I had exactly the same problem. The PDF files would open with ezPDF and Adobe but not with Polaris Viewer. You have to set the data and type with:
intent.setDataAndType(uri, "application/pdf");
instead of using:
intent.setType("application/pdf");
intent.setData(uri);
For me the following is working fine with Polaris now:
Uri uri = FileProvider.getUriForFile(MyApplication.getContext(), MyApplication.getContext().getPackageName() + ".myfileprovider", destFile);
Intent intent = new Intent(Intent.ACTION_VIEW);
intent.setDataAndType(uri, "application/pdf");
intent.addFlags(Intent.FLAG_GRANT_READ_URI_PERMISSION);
startActivity(intent);