I don't see why one is exclusive of the other, do you?
If God does orchestrate a series of "natural event"'s in order to glorify Him and His Son and he is the creator of the world then it might be impossible to separate what we would perceive as the natural from the supernatural except that we would never quite be able to replicate, understand or even know what the exact physical forces which were used at that moment in time.
These events would be the result of what the rational mind would attribute to a "fluke" or a false witness or a mistaken observation or a miracle.
Continuing with the "if". If God created this complex world in six days, how much harder for him to place within it a set of supernatural events in the context of his foreknowledge of the events to come. (He is outside of time). This would allow that his creation could put forth the unexpected and the impossible without violating the laws of our physical world. The miracle then is the presence of witnesses and the correlation of the event for the purposes of God's glory.
To the extent we begin to understand the processes which come into play that caused the many miracles we can appreciate the awesome power God has to create. However, some who believe they understand the process used may then think of themselves as greater than God. They fail to see that causing the miracle was the easy part. Having it occur at the precise time and place in history is the real miracle.
The question was
"Do you agree that an event having the appearance of being a miracle may later be found to have a natural explanation?"
You are submitting that you do not agree that an event that has the appearance of being a miracle may later be found to have a natural explanation, because there are events in the Bible that cannot be explained by natural causes.
IOW, you're arguing that if any event has the initial appearance of being a miracle (ie happening contrary to known natural laws), then it must be one and there will never be a natural explanation for it, because the Bible describes events that can only be described as miracles.