Before the final acceptance, I have already paid 99%, so what should I still withhold?
Let me try to explain the whole thing to you; this has nothing to do with your actual question or whether 99% is appropriate or not.
According to the contract, you owe 99% of the construction sum upon acceptance. So far so good. Before the planned acceptance, you should walk through the house with an expert. During this, you check whether a) the house is finished and b) free of defects. Only when a) and b) are fulfilled do you pay the 99% and then the acceptance follows. If the house is not finished, there is no acceptance and no 99%. Instead, you issue a request to the builder to finally finish the construction (with a deadline). If there are defects, you have to decide (the expert helps here) whether the defects are so severe that they oppose acceptance. Then there is no acceptance and no 99%. If they are minor defects, then you have the right to withhold double (or 2 to 3 times) the cost of defect remediation. Then you pay 99% minus 2 to 3 times the cost of defect remediation. The expert helps determine these costs. When enforcing your rights (i.e., so that the builder does not cause trouble), a specialist lawyer for construction law may help.
Even better than this theory is, of course, a payment plan favorable to you from the start. 95% is better than 99%. But in the end, it is not as important as in between. If your builder goes bankrupt at 99%, then it does not matter. At 50% shell construction and insolvency of the builder, you would have a serious problem.