Grammatical number of Latin nouns used attributively before other nouns
Solution 1:
Your suggestion using stratum is logically sound, but unfortunately the reality is that it isn't totally consistent. With words that have clearly marked plurals, we can see that we use singular, e.g. multicolor. However, we also have words like the well-established multimedia. The pattern seems to fall apart sometimes in places where the plural is irregular. Not always, but sometimes. (I am sure that is very unsatisfying!)
Solution 2:
A search in Google suggests that "multi-stratal" is widely used. Another example: "fungal species".