Absolutely. Very difficult to compare. The similarities/differences will depend on which specific systems are being compared.
However, I would guess that, in general, Silat systems would have more in common with FMA from the southern PI than from the central/northern.
90% of the FMA training I have comes from central/northern PI systems. 90% of the Silat training I have comes from Javanese systems. In my personal experience, there are definitely some technical similarities - but the mindset between the two is very different. To give an example: in the FMA that I've trained, we generally try to avoid getting hit/cut/stuck if we can. We know it's probably going to happen but we work a lot of evasion (usually done in an aggressive manner that helps us take control of the weapon and start finishing the attacker - but still evasion-based). In the Silat that I've seen, most of it is pretty non-evasive. In fact, one of my instructors said once, "someone tries to stab you, guide the knife into your chest and sheath it on the outside of your ribs, then pin it there while you kill him." So, basically, "stab yourself - but it's only a flesh wound - then kill him." That's very much the Silat mindset that I've been exposed to. It basically boils down to, "I don't care what you do. I'm going to kill you regardless of what you do or try to do to me." (this is, of course, in some ways an oversimplification but that's the gist). The FMA that I've trained in have a mindset of "deal with the weapon, finish the man." In application, the line between these mindsets is sometimes pretty thin and may even vanish completely but it does change the training some - it's like seasoning a stew with jalapeno vs. jabanero. It's the same type of seasoning but there is definitely a difference.
At least, that's my take on it based on my personal experiences. Milage is guaranteed to differ from person to person simply because we each have different backgrounds/experiences in FMA and Silat.
Mike