If you're referring to the blobby stuff on top, that's normal: it's a sealant. It appears yours has done what many high-use flybacks of this era have done and turned brown with age / heat / etc. Your also appears to be cracked. All of which suggests this transformer is nearing the end of This could be the source of your flickering. Are you noticing a ringing sound, or an ozone smell?
If you're referring to the bottom, that does indeed appear to be rust and is not normal, but not uncommon either. I suppose there is a chance that it's interfering with the circuit... but given the overall state of it, you might want to keep an eye out for a parts analog board from a Plus / SE / SE/30 that you can source another transformer from.