iopq wrote:

The rules say: "The analysis is a move-sequence continuing the alternation"

Therefore, you cannot make a general statement like this. First of all, the analysis allows the players' mistakes. Therefore, at least you have to make the assumption of perfect play by both players during the analysis. Furthermore, before you can make one statement for the outcome of a perfectly played analysis, you have to study two cases:

1) Games in which the analysis starts by Black.

2) Games in which the analysis starts by White.

Next, note that three-points-without-capturing involves possibility for ko fights. Therefore, perfect play depends on the rest of the board. Therefore, three-points-without-capturing is NOT a simple local position in which there would always be the same perfect play for a given starting player, and so for either starting player. Hence, under the Simplified Japanese Rules, you may not make the general statement that three-points-without-capturing (with a single black stone and 4 white stones) was worth 2 points.

Instead, the evaluation depends on how the players play the analysis.

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since otherwise it's alive

The Simplified Japanese Rules do not use the term "alive". They use the term "independently alive". To apply rules, do not alter them.

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if the player agreed

Agreement is something done by both players.

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to go to analysis he can no longer go back and fix the situation since playing it out before analysis yields more points?

The rules say: "The game consists of the alternation, then the optional analysis, and then the game end."

Therefore, a) there is exactly one alternation, at most one analysis and exactly one game end, b) the alternation precedes the analysis.

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Also, can you easily just retrofit a rule that says "territory is surrounded only by independently alive stones" to simulate Japanese no territory in seki rule? Isn't that just as simple as the territory in seki rule?

It is possible to make the rules less simplified, e.g., by adding a "seki" exception. See some of my other rulesets for how to do so.