So one malformed base and he changes the game's rules, versus I don't know, replacing that one base?

This is what I am saying. There is even a rule about damaged game components. Did no one have a spare small or large base lying around to let the guy use?

So the TO is running a casual event using a game night or store tourney kit?

It says in the rules that TOs running casual events have the right to organize the event as they see fit. This is so TOs can implement house rules. Premiere events, or rather events which the TO chooses to take more seriously obviously require strict adherence to the rules.

At a casual event you should be prepared to be flexible with not only the TO and the format but with other players as well. The format of a casual event should be decided by the TO.

When I run events, even casual ones I demand proper rules enforcement and adherence to good sportsmanship. Even when we do alternative formats I still expect my players to behave as if they were at a world class event. That is an expectation I have for all my events and some people don't like that, but if they don't well then the Magic cards are over there.

If you are so concerned with this house rule, get some like minded people together to talk to the TO and explain why his ruling has a negative effect on gameplay. Demonstrate the effects of the rule and show how it negatively impacts your playstyle and that of others and explain why you think it should be abolished.

I'm sure of you talk to the guy he will relent or at least work with you to alleviate the problems. If your TO refuses to accomodate you then don't play in the event. Simple as that.

Straight from the RRG

"Guides

Each ship's base has two pairs of movement guides, one pair on the front and one pair on the back. These guides are ignored for all purposes except executing maneuvers and overlapping obstacles and other ships. In those cases, the guides count as part of the base."

Also, the section on Range states clearly that you measure base to base:

"Range

Range is the distance between two ships as measured by the range ruler, which is divided into three range bands. To measure range between two ships, place the range ruler over the point of the first ship that is closest to the second ship, then point the other end of the ruler toward the point of the second ship's base that is closest to the first base. The range is the band of the range ruler that falls over the closest point of the second ship."

If it's an official event, they should only change the rules when they find a contradiction or error, but this isn't really one of those cases. If he's doing this because of one malformed base then he should request a replacement of the base and randomly check bases (but that seems like major overkill).

it's a casual event so he can choose. Just looking at my falcon card boards on top of each other and they are all cut slightly different. So really his cardboard to cardboard Idea is silly too.

Aren't the cardboard tokens more rectangular compared to the square plastic bases