It turns out that this is a bug. Using a value like 50% for smooth scrolling articles works on iOS but not Android.
The workaround is to use the page method (#n) instead of a percentage to jump to a specific location. In a smooth scrolling article, each tile, or screen, is effectively a page. So if you have a 6-tile smooth scrolling article (such as 768x6000), you would use something like navto://relative/current#2 to jump to tile 3 of the smooth scrolling article. You can use decimal point (#2.3) to fine-tune the link.
I'll try to remember to reply to this thread when the Android viewer bug is fixed.