Help with Transparency Flattener!

I'm working with an Indesign file that has Illustrator links, which contain gradient meshes that use transparency. When I export my Indesign file, the transparency flattener does something very strange to the gradient mesh: it displays the vector lines of the mesh as dark grey lines.
I've found a way around this problem, but it is not ideal. If I export the file as Acrobat 4, I can change the transparancy flattener settings, and eliminate the issue. However, if I use Acrobat 4, I also lose the ability to add hyperlinks in the document (of which I have a number) Why is that that if you use a higher version of acrobat (5 or above) you suddenly lose the ability to manage the transparancy flattener? Why would older versions of the product allow more freedom and control?
Any help would be greatly appreciated. Below are screeshots of what it looks like in illustrator, and then flattened but the default flatteners of acrobat 5 and above. Really, I just want to be able to achieve a customized flattener that doesn't contain those dark lines, but not have to use actobat 4 to do it.
Thanks!
jason

Hi Steve—
Your questions have half solved my problem for me!
I'm using the latest version of Indesign (7.5) and Illustrator (15.1.0)
I'm exporting using the High Quality Print setting (I know, a bit strange to use this setting AND want hyperlinks, but the PDF is intended for web distribution to people who might decide to print it) and when I choose anything above acrobat 4 in the compatibility drop down (5, 6, 7...) then the transparency flattener is greyed out in the advanced tab, with medium set as the default. If i want to choose my own flattener settings, I have to go with PDF 4, at which point I lose hyperlinks. I've also tried exporting choosing Adobe PDF (Interactive) from the initial menu, but that results in the same lines in the gradient mesh.
However, it turns out this issue is only happening when viewing the pdf in apple's preview app. It actually looks fine in acrobat. However, seeing as how Preview is the default app for viewing PDFs on a mac, I'm concerned that a bulk of our audience will be seeing it this way.
I know this likely puts things out of the realm of adobe, but if you have any wisdom to impart,  I'd appreciate it. Attached is what the file looks like viewed acrobat (above) and preview (below).
thanks!
jason

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