As others have mentioned spot facing to achieve a flat surface to reduce deflection is always desirable. However I do not know if you have the option to do that step. I personally was not following everything you had going on. At first I just thought you had a couple of cylinders to drill. Now that we have more information we can see that this is probably one of several machining steps that you are performing to the cylinders with the rotary transfer machine. I still do not see the whole picture with the rotary transfer machine and beings I am not familiar with this equipment I do not understand its full capabilities. Example we do not know if you have other units around the table that can be utilized? You said that the cylinder was chucked in a fixed position so in order to achieve a 45º angle you must be able to rotate a drilling unit separately on that angle in relationship to the cylinder position. Please confirm?
Again, I may not being following everything that is going on here. But based on our known information that you only have one drilling unit non-CNC that only has X and Y positioning, we have to assume that you are limited to one step in drilling your hole. I do not understand fully what ve7brz is saying but he is on the right track as far as locating to the cylinder with a guide. "IF" your drilling unit can be rotated around to a 45º angle relative to the position of the cylinder than I can only see one way of drilling while minimizing drill deflection.
I would have you machine shop fabricate a two piece spring loaded, locating drill guide. This device would be fixed to the drill unit and move along the z-axis with the drill bit. I feel like ve7brz locating to the cylinder is the only way to go. Depending on how design creative you team gets you could even have replaceable drill bushings as part of your design. Down and dirty the springs allow you to delay the engagement of drill to the surface. 1) The face of the guide would engage to the cylinder wall for location. 2) The drill unit would continue to advance compressing the springs and moving the drill through the bushing guide to make contact to the cylinder surface and drill the hole. The only kicker here is not knowing how repeatable the positioning of the cylinder to the drilling unit is. This of course will drive the design styling of engagement face, drill deflection and bushing wear.