So getting a penalty in football would be the equivalent of calling the infraction in disc golf but seconding it would be like accepting the penalty and not declining it. At least that's how I'm reading what you posted. If not calling it or calling it to gain a strategic advantage over your opponent is what you're trying to do than I see that as just playing to win via loophole and not actually with a disc.
It can be seen that way yes. While it may be more honorable to play the rules as people generally agree they should be played, there is no shame in understanding and using the actual rules to your advantage, particularly at higher levels of play. If you feel your honor is infringed upon by playing this way, you could either A) not play this way and hope your opponents don't either or B) inform your opponents that you are going to be a stickler to the rules ahead of time so they know you treat disc golf like any other sport with a rulebook. If enough people feel that this rule is unjust or "not cool" then there will be a movement and it will be changed. Until then, it's foolish not to take every advantage you can. Don't get me wrong, I am actually really lax about this in casual play, but during a tourney you should follow the rules.