My aluminum roof is 44 years old and doesn't leak. It did take about 20 hrs. of scraping old roofing tar/silicone/other sealants and two rolls of Eternabond to get it leak proof.
Mold on EPDM is not going to ruin the roof. If you clean the roof with an algacide it should be good for many years. Most leak problems are caused at the penetrations through the EPDM and the sealant failing. If you park in an area under trees you'll have more growth on the roof. Cuprous and zinc oxides are known to inhibit fungus or algae, that is why cedar shingle roofs with a copper ridge cap rarely have fungus, algae or moss growing on the shingles. Figure out a way to get some copper or zinc on the roof and you won't have "mold" on the roof.