For the Caramel. Add the sugar and water to a saucepan. Melt over high heat and let it simmer until amber colour. Swirl the pan to evenly distribute the heat (to avoid burning the caramel) until golden brown. Immediately remove from heat and pour into the baking pan.
For the Flan. In a medium-sized bowl, whisk the whole eggs, egg yolks, pure vanilla extract and lemon zest. Add the whole milk and condensed milk. Mix until well blended and set aside.
Preheat the oven while making the vanilla chiffon cake. For the cake batter. In a large bowl, add all the wet ingredients. Mix until well blended. Sift the dry ingredients over the wet ingredient mixture. Mix until smooth
Make the meringue. In a stand mixer bowl, beat the room temperature egg whites and cream of tartar at high speed while gradually adding sugar. Beat until stiff peaks.
Slowly add the cake batter to the meringue or add in four additions. Using a spatula or whisk in folding-scraping motion until no streaks of cake batter. Tap to remove some air bubbles.
Layering the custard cake. With the fine mesh strainer, pour the flan mixture into the baking pan with the caramel that has been cooled. Add and pour the vanilla chiffon cake batter over the flan mixture. Use a cake tester or toothpick and swirl the cake batter to remove some air bubbles and to even out the top.
Bake the Custard Cake. Place at the lower rack of the preheated oven inside the rectangular baking pan. Pour the hot water into the rectangular baking pan, steam and bake at 350°F for 50 to 55 minutes.
Cooling the cake. Remove the cake from the oven and place it on a cooling rack. Let it cool in the pan but still warm to the touch for about 15 to 30 minutes max.
Transfer the custard cake inverted on a cake server. Tastes best when served chilled.